Starting phenix.real_space_refine on Sun Mar 3 13:12:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abz_11710/03_2024/7abz_11710_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abz_11710/03_2024/7abz_11710.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abz_11710/03_2024/7abz_11710_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abz_11710/03_2024/7abz_11710_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abz_11710/03_2024/7abz_11710_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abz_11710/03_2024/7abz_11710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abz_11710/03_2024/7abz_11710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abz_11710/03_2024/7abz_11710_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abz_11710/03_2024/7abz_11710_updated.pdb" } resolution = 3.21 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 5017 5.49 5 Mg 192 5.21 5 S 166 5.16 5 C 78986 2.51 5 N 29164 2.21 5 O 43701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 ARG 59": "NH1" <-> "NH2" Residue "5 ARG 86": "NH1" <-> "NH2" Residue "5 ARG 88": "NH1" <-> "NH2" Residue "5 ARG 103": "NH1" <-> "NH2" Residue "5 ARG 153": "NH1" <-> "NH2" Residue "6 GLU 3": "OE1" <-> "OE2" Residue "6 ARG 123": "NH1" <-> "NH2" Residue "6 ARG 154": "NH1" <-> "NH2" Residue "6 ARG 171": "NH1" <-> "NH2" Residue "6 ARG 223": "NH1" <-> "NH2" Residue "6 ARG 233": "NH1" <-> "NH2" Residue "6 ARG 269": "NH1" <-> "NH2" Residue "6 ARG 279": "NH1" <-> "NH2" Residue "6 ARG 288": "NH1" <-> "NH2" Residue "6 ARG 318": "NH1" <-> "NH2" Residue "6 ARG 373": "NH1" <-> "NH2" Residue "6 ARG 377": "NH1" <-> "NH2" Residue "6 ARG 381": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G GLU 114": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 31": "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 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 21": "NH1" <-> "NH2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 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 3": "NH1" <-> "NH2" Residue "T ARG 12": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 48": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 12": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 4": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g GLU 169": "OE1" <-> "OE2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h ARG 107": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "i ARG 47": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 99": "NH1" <-> "NH2" Residue "n ARG 109": "NH1" <-> "NH2" Residue "n ARG 119": "NH1" <-> "NH2" Residue "n ARG 124": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 31": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "q ARG 56": "NH1" <-> "NH2" Residue "q ARG 121": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r GLU 72": "OE1" <-> "OE2" Residue "r ARG 98": "NH1" <-> "NH2" Residue "r ARG 101": "NH1" <-> "NH2" Residue "s ARG 24": "NH1" <-> "NH2" Residue "s ARG 41": "NH1" <-> "NH2" Residue "s ARG 53": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 75": "NH1" <-> "NH2" Residue "t ARG 84": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u GLU 47": "OE1" <-> "OE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "x ARG 81": "NH1" <-> "NH2" Residue "z ARG 55": "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: 157227 Number of models: 1 Model: "" Number of chains: 66 Chain: "1" Number of atoms: 62355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2904, 62355 Classifications: {'RNA': 2904} Modifications used: {'rna2p': 6, 'rna2p_pur': 277, 'rna2p_pyr': 151, 'rna3p': 16, 'rna3p_pur': 1389, 'rna3p_pyr': 1064} Link IDs: {'rna2p': 434, 'rna3p': 2469} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 33048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33048 Classifications: {'RNA': 1540} Modifications used: {'rna2p': 1, 'rna2p_pur': 118, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 750, 'rna3p_pyr': 572} Link IDs: {'rna2p': 208, 'rna3p': 1331} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "3" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 102} Chain: "4" Number of atoms: 7760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 7760 Classifications: {'RNA': 363} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 41, 'rna2p_pyr': 27, 'rna3p': 2, 'rna3p_pur': 157, 'rna3p_pyr': 135} Link IDs: {'rna2p': 69, 'rna3p': 293} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "5" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1181 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "6" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2871 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "7" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1635 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p': 7, 'rna3p_pur': 31, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 65} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 1 Chain: "8" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 327 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna2p': 8, 'rna3p': 6} Chain: "A" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 601 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" 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: "D" 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: "E" 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: "F" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1322 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 470 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} 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: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} 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: "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: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} 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: "b" 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: "c" 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: "d" 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: "e" 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: "f" 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: "g" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "h" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "i" 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: "j" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1118 Classifications: {'peptide': 152} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 146} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "l" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" 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: "n" 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: "o" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "p" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" 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: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" 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: "u" 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: "v" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "x" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "y" 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: "z" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 466 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "1" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 168 Unusual residues: {' MG': 168} Classifications: {'undetermined': 168} Link IDs: {None: 167} Chain: "2" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' MG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'GDP': 1, 'KIR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0TCX SG CYS f 11 168.386 181.421 88.498 1.00101.96 S ATOM A0TDM SG CYS f 14 171.659 180.391 90.140 1.00102.90 S ATOM A0TGH SG CYS f 27 169.715 183.430 91.503 1.00 99.76 S Time building chain proxies: 58.97, per 1000 atoms: 0.38 Number of scatterers: 157227 At special positions: 0 Unit cell: (295.35, 254.538, 240.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 166 16.00 P 5017 15.00 Mg 192 11.99 O 43701 8.00 N 29164 7.00 C 78986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS q 34 " - pdb=" SG CYS q 53 " distance=2.74 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: 68.95 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " Number of angles added : 3 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11580 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: 189 helices and 73 sheets defined 38.2% alpha, 18.8% beta 1545 base pairs and 2414 stacking pairs defined. Time for finding SS restraints: 76.67 Creating SS restraints... Processing helix chain '5' and resid 17 through 24 removed outlier: 4.525A pdb=" N TYR 5 24 " --> pdb=" O ALA 5 20 " (cutoff:3.500A) Processing helix chain '5' and resid 41 through 47 removed outlier: 6.714A pdb=" N ARG 5 45 " --> pdb=" O VAL 5 41 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA 5 46 " --> pdb=" O LYS 5 42 " (cutoff:3.500A) Processing helix chain '5' and resid 97 through 106 Processing helix chain '5' and resid 138 through 155 removed outlier: 4.341A pdb=" N LYS 5 143 " --> pdb=" O ARG 5 139 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET 5 155 " --> pdb=" O LYS 5 151 " (cutoff:3.500A) Processing helix chain '6' and resid 23 through 40 Processing helix chain '6' and resid 87 through 99 removed outlier: 3.937A pdb=" N THR 6 93 " --> pdb=" O LYS 6 89 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP 6 99 " --> pdb=" O ALA 6 95 " (cutoff:3.500A) Processing helix chain '6' and resid 112 through 126 Processing helix chain '6' and resid 136 through 141 removed outlier: 3.845A pdb=" N VAL 6 140 " --> pdb=" O LYS 6 136 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP 6 141 " --> pdb=" O CYS 6 137 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 136 through 141' Processing helix chain '6' and resid 142 through 161 removed outlier: 5.455A pdb=" N LEU 6 146 " --> pdb=" O ASP 6 142 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU 6 147 " --> pdb=" O GLU 6 143 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 180 removed outlier: 3.985A pdb=" N ALA 6 177 " --> pdb=" O SER 6 173 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU 6 178 " --> pdb=" O ALA 6 174 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU 6 179 " --> pdb=" O LEU 6 175 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY 6 180 " --> pdb=" O LYS 6 176 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 173 through 180' Processing helix chain '6' and resid 181 through 200 removed outlier: 5.250A pdb=" N GLU 6 185 " --> pdb=" O ASP 6 181 " (cutoff:3.500A) Proline residue: 6 200 - end of helix Processing helix chain '6' and resid 282 through 287 removed outlier: 4.847A pdb=" N GLU 6 287 " --> pdb=" O ARG 6 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 7.580A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.540A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.174A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.724A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 6.522A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 5.666A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.632A pdb=" N ALA C 102 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 41 removed outlier: 5.352A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 removed outlier: 4.131A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 4.463A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 5.659A pdb=" N ASP D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'E' and resid 2 through 20 removed outlier: 4.159A pdb=" N TYR E 7 " --> pdb=" O LYS E 3 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 12 " --> pdb=" O TYR E 8 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 removed outlier: 4.220A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 97 through 112 removed outlier: 4.317A pdb=" N GLU E 101 " --> pdb=" O TRP E 97 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix removed outlier: 4.845A pdb=" N ARG E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 removed outlier: 4.202A pdb=" N ARG E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 removed outlier: 5.774A pdb=" N ASP E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 174 removed outlier: 4.851A pdb=" N LEU E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 81 removed outlier: 6.817A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 151 removed outlier: 4.187A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 34 removed outlier: 4.692A pdb=" N VAL G 31 " --> pdb=" O ARG G 27 " (cutoff:3.500A) Proline residue: G 32 - end of helix Processing helix chain 'G' and resid 40 through 50 Processing helix chain 'G' and resid 51 through 73 removed outlier: 4.402A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU G 70 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 111 through 116 removed outlier: 5.493A pdb=" N ARG G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 removed outlier: 3.707A pdb=" N GLN H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 33 removed outlier: 3.939A pdb=" N VAL H 33 " --> pdb=" O ASP H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 4.643A pdb=" N GLU H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 65 removed outlier: 3.929A pdb=" N ALA H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 106 removed outlier: 3.683A pdb=" N ALA H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 78 removed outlier: 6.103A pdb=" N PHE H 76 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL H 77 " --> pdb=" O ASP H 74 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY H 78 " --> pdb=" O ALA H 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 73 through 78' Processing helix chain 'I' and resid 76 through 82 removed outlier: 4.379A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 111 removed outlier: 4.086A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.969A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.476A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.718A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 135 removed outlier: 4.440A pdb=" N ALA J 133 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 119 removed outlier: 6.305A pdb=" N MET K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 42 removed outlier: 5.069A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 7.070A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 84 removed outlier: 3.642A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.290A pdb=" N LYS M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.743A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.603A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.816A pdb=" N THR N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.992A 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: 4.293A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.293A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.528A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 Processing helix chain 'P' and resid 97 through 104 removed outlier: 5.711A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.626A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.553A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.965A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.760A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 4.110A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 60 removed outlier: 3.612A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 4.006A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.760A 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 3 through 11 removed outlier: 3.867A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 6.459A pdb=" N SER T 21 " --> pdb=" O SER T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.769A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.537A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 3.994A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 removed outlier: 3.727A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.620A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'b' and resid 9 through 21 removed outlier: 3.529A pdb=" N ARG b 13 " --> pdb=" O THR b 9 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 3.920A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.683A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 52 through 63 removed outlier: 4.097A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 24 through 29 removed outlier: 3.921A pdb=" N LYS g 28 " --> pdb=" O ASN g 24 " (cutoff:3.500A) Proline residue: g 29 - end of helix No H-bonds generated for 'chain 'g' and resid 24 through 29' Processing helix chain 'g' and resid 44 through 64 Proline residue: g 48 - end of helix Processing helix chain 'g' and resid 74 through 88 removed outlier: 5.428A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER g 86 " --> pdb=" O ASP g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 103 removed outlier: 4.679A pdb=" N LEU g 101 " --> pdb=" O LEU g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 123 Processing helix chain 'g' and resid 130 through 149 removed outlier: 7.425A pdb=" N ALA g 134 " --> pdb=" O THR g 130 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU g 135 " --> pdb=" O LYS g 131 " (cutoff:3.500A) Processing helix chain 'g' and resid 150 through 155 removed outlier: 5.048A pdb=" N MET g 154 " --> pdb=" O GLY g 150 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY g 155 " --> pdb=" O ILE g 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 150 through 155' Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 226 removed outlier: 3.701A pdb=" N GLY g 224 " --> pdb=" O THR g 220 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG g 225 " --> pdb=" O VAL g 221 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.842A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 Processing helix chain 'h' and resid 72 through 78 Processing helix chain 'h' and resid 81 through 96 Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.337A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.963A pdb=" N GLY h 145 " --> pdb=" O ALA h 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.456A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU i 15 " --> pdb=" O LEU i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 66 removed outlier: 6.514A pdb=" N GLN i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 4.672A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 Processing helix chain 'i' and resid 146 through 152 removed outlier: 3.665A pdb=" N LYS i 150 " --> pdb=" O ARG i 146 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN i 152 " --> pdb=" O LYS i 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 146 through 152' Processing helix chain 'i' and resid 153 through 166 removed outlier: 3.857A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 5.052A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.170A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.636A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 6.515A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL j 114 " --> pdb=" O ALA j 110 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 5.480A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'k' and resid 11 through 33 removed outlier: 4.099A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) Proline residue: k 19 - end of helix Processing helix chain 'k' and resid 67 through 81 Processing helix chain 'l' and resid 20 through 31 removed outlier: 4.640A pdb=" N ALA l 24 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN l 28 " --> pdb=" O ALA l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.800A pdb=" N ALA l 61 " --> pdb=" O SER l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.910A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.545A pdb=" N ARG l 119 " --> pdb=" O SER l 115 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 150 removed outlier: 4.376A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA l 147 " --> pdb=" O ARG l 143 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS l 149 " --> pdb=" O ALA l 145 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA l 150 " --> pdb=" O GLU l 146 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 removed outlier: 3.876A pdb=" N GLU m 43 " --> pdb=" O VAL m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 40 removed outlier: 5.504A pdb=" N GLY n 40 " --> pdb=" O GLU n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 43 through 53 removed outlier: 4.037A pdb=" N VAL n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) Proline residue: n 51 - end of helix Processing helix chain 'n' and resid 71 through 92 Processing helix chain 'n' and resid 94 through 102 Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.603A pdb=" N ILE o 18 " --> pdb=" O ASP o 14 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 5.916A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA o 86 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG o 89 " --> pdb=" O ASP o 85 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU o 90 " --> pdb=" O ALA o 86 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.218A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 59 through 76 removed outlier: 4.723A pdb=" N VAL p 74 " --> pdb=" O CYS p 70 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 104 removed outlier: 6.239A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 Processing helix chain 'r' and resid 14 through 23 removed outlier: 3.721A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 44 through 49 removed outlier: 3.711A pdb=" N LEU r 48 " --> pdb=" O LYS r 44 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER r 49 " --> pdb=" O ILE r 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 44 through 49' Processing helix chain 'r' and resid 50 through 64 removed outlier: 4.475A pdb=" N THR r 55 " --> pdb=" O GLY r 51 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU r 56 " --> pdb=" O GLN r 52 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 Processing helix chain 'r' and resid 85 through 94 Processing helix chain 's' and resid 3 through 27 removed outlier: 4.920A pdb=" N ALA s 22 " --> pdb=" O ASP s 18 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS s 23 " --> pdb=" O LYS s 19 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG s 24 " --> pdb=" O TYR s 20 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU s 27 " --> pdb=" O LYS s 23 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 34 Processing helix chain 's' and resid 41 through 51 removed outlier: 5.145A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 47 removed outlier: 4.032A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU t 45 " --> pdb=" O GLY t 41 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N HIS t 46 " --> pdb=" O HIS t 42 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS t 47 " --> pdb=" O PHE t 43 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 79 Processing helix chain 'w' and resid 25 through 34 removed outlier: 5.191A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 Processing helix chain 'x' and resid 12 through 25 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.878A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 8 through 41 Processing helix chain 'y' and resid 44 through 65 removed outlier: 3.759A pdb=" N GLN y 48 " --> pdb=" O LYS y 44 " (cutoff:3.500A) Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.733A pdb=" N LYS y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU y 86 " --> pdb=" O GLN y 82 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 3.511A pdb=" N LEU z 16 " --> pdb=" O PHE z 12 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 36 removed outlier: 4.364A pdb=" N VAL z 32 " --> pdb=" O VAL z 28 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU z 36 " --> pdb=" O VAL z 32 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 57 Processing sheet with id= 1, first strand: chain '5' and resid 28 through 33 removed outlier: 4.026A pdb=" N GLU 5 28 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE 5 30 " --> pdb=" O ILE 5 127 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE 5 127 " --> pdb=" O PHE 5 30 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA 5 32 " --> pdb=" O VAL 5 125 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS 5 126 " --> pdb=" O LEU 5 114 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY 5 108 " --> pdb=" O GLY 5 132 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '6' and resid 63 through 71 removed outlier: 6.942A pdb=" N ASN 6 63 " --> pdb=" O PRO 6 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS 6 75 " --> pdb=" O PRO 6 10 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLY 6 18 " --> pdb=" O CYS 6 81 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL 6 104 " --> pdb=" O ILE 6 17 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA 6 106 " --> pdb=" O HIS 6 19 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '6' and resid 210 through 214 removed outlier: 6.705A pdb=" N PHE 6 210 " --> pdb=" O LYS 6 294 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLN 6 290 " --> pdb=" O ILE 6 214 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU 6 240 " --> pdb=" O CYS 6 255 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '6' and resid 216 through 220 removed outlier: 3.674A pdb=" N ASP 6 216 " --> pdb=" O THR 6 228 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR 6 225 " --> pdb=" O LEU 6 278 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '6' and resid 304 through 308 removed outlier: 4.010A pdb=" N ILE 6 356 " --> pdb=" O VAL 6 308 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL 6 337 " --> pdb=" O PHE 6 330 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU 6 372 " --> pdb=" O VAL 6 388 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY 6 384 " --> pdb=" O ILE 6 376 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '6' and resid 305 through 310 removed outlier: 6.673A pdb=" N GLU 6 305 " --> pdb=" O ALA 6 389 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA 6 385 " --> pdb=" O TYR 6 309 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.663A pdb=" N ILE A 80 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 48 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 82 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.668A pdb=" N PHE A 60 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= 10, first strand: chain 'B' and resid 33 through 36 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.916A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLN B 117 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.017A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 90 through 96 removed outlier: 5.834A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 106 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 3 through 7 removed outlier: 5.946A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.579A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG C 179 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.610A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 1 through 6 removed outlier: 3.821A pdb=" N MET D 1 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 42 through 47 removed outlier: 7.223A pdb=" N GLY D 42 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASP D 91 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG D 44 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA D 87 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 117 through 120 Processing sheet with id= 20, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.677A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS E 87 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL E 89 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE E 34 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LYS E 33 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE E 156 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N THR E 35 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE E 154 " --> pdb=" O THR E 35 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 22, first strand: chain 'F' and resid 41 through 45 removed outlier: 4.526A pdb=" N GLY F 53 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 82 through 89 removed outlier: 5.845A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'F' and resid 94 through 98 removed outlier: 3.853A pdb=" N VAL F 113 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 76 through 81 removed outlier: 6.347A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL G 78 " --> pdb=" O ILE G 143 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'H' and resid 22 through 27 removed outlier: 4.610A pdb=" N VAL H 27 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ALA H 83 " --> pdb=" O VAL H 27 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 52 through 57 removed outlier: 5.375A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 74 through 78 removed outlier: 4.124A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.869A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 62 through 66 removed outlier: 6.384A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 71 through 74 Processing sheet with id= 32, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.879A pdb=" N ALA N 108 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE N 102 " --> pdb=" O ALA N 108 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 49 through 52 Processing sheet with id= 34, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.872A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.706A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 37, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.117A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 39, first strand: chain 'R' and resid 71 through 78 removed outlier: 3.983A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.619A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY S 79 " --> pdb=" O THR S 100 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'T' and resid 29 through 33 removed outlier: 3.694A pdb=" N GLY T 75 " --> pdb=" O LYS T 68 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS T 68 " --> pdb=" O GLY T 75 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 40 through 45 removed outlier: 5.041A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 83 through 87 removed outlier: 5.739A pdb=" N ARG U 94 " --> pdb=" O ILE U 103 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 26 through 31 removed outlier: 6.546A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.512A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 47, first strand: chain 'Z' and resid 33 through 39 removed outlier: 3.997A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.244A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 19 through 24 removed outlier: 5.893A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.672A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'f' and resid 1 through 5 removed outlier: 6.482A pdb=" N HIS f 33 " --> pdb=" O CYS f 27 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N CYS f 27 " --> pdb=" O HIS f 33 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 89 through 93 removed outlier: 3.731A pdb=" N GLY g 71 " --> pdb=" O VAL g 92 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'h' and resid 19 through 22 removed outlier: 5.993A pdb=" N ASN h 19 " --> pdb=" O ILE h 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR h 21 " --> pdb=" O ILE h 57 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ARG h 59 " --> pdb=" O THR h 21 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 164 through 169 removed outlier: 6.143A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'i' and resid 140 through 145 removed outlier: 6.105A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TRP i 170 " --> pdb=" O LYS i 183 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 12 through 16 removed outlier: 7.166A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 83 through 88 removed outlier: 7.616A pdb=" N HIS j 83 " --> pdb=" O PRO j 98 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 33 through 40 removed outlier: 4.701A pdb=" N GLY j 51 " --> pdb=" O ALA j 35 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 38 through 42 removed outlier: 3.804A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU k 40 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU k 61 " --> pdb=" O GLU k 40 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP k 42 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.567A pdb=" N ARG k 45 " --> pdb=" O ALA k 57 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA k 57 " --> pdb=" O ARG k 45 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU k 47 " --> pdb=" O HIS k 55 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 72 through 79 removed outlier: 6.182A pdb=" N THR l 72 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.300A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.667A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'n' and resid 5 through 11 Processing sheet with id= 65, first strand: chain 'o' and resid 39 through 42 removed outlier: 4.721A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE o 8 " --> pdb=" O VAL o 74 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER o 101 " --> pdb=" O ARG o 7 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 67, first strand: chain 'p' and resid 42 through 45 removed outlier: 4.489A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 29 through 32 removed outlier: 3.561A pdb=" N GLY q 32 " --> pdb=" O ILE q 80 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 36 through 41 removed outlier: 3.618A pdb=" N ARG q 50 " --> pdb=" O THR q 40 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE q 61 " --> pdb=" O LEU q 57 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'u' and resid 16 through 20 Processing sheet with id= 71, first strand: chain 'v' and resid 7 through 11 removed outlier: 7.067A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'v' and resid 20 through 31 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'x' and resid 30 through 34 2038 hydrogen bonds defined for protein. 6018 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3903 hydrogen bonds 6196 hydrogen bond angles 0 basepair planarities 1545 basepair parallelities 2414 stacking parallelities Total time for adding SS restraints: 245.86 Time building geometry restraints manager: 74.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 12837 1.25 - 1.40: 50846 1.40 - 1.54: 96041 1.54 - 1.68: 10598 1.68 - 1.83: 298 Bond restraints: 170620 Sorted by residual: bond pdb=" N PRO x 59 " pdb=" CD PRO x 59 " ideal model delta sigma weight residual 1.473 1.682 -0.209 1.40e-02 5.10e+03 2.23e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.436 -0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C5 5MU 4 341 " pdb=" C6 5MU 4 341 " ideal model delta sigma weight residual 1.155 1.435 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.435 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C5 5MU 7 54 " pdb=" C6 5MU 7 54 " ideal model delta sigma weight residual 1.155 1.431 -0.276 2.00e-02 2.50e+03 1.91e+02 ... (remaining 170615 not shown) Histogram of bond angle deviations from ideal: 75.15 - 91.92: 7 91.92 - 108.69: 63250 108.69 - 125.45: 172827 125.45 - 142.22: 19139 142.22 - 158.99: 10 Bond angle restraints: 255233 Sorted by residual: angle pdb=" C3' A 12439 " pdb=" C2' A 12439 " pdb=" O2' A 12439 " ideal model delta sigma weight residual 114.60 83.12 31.48 1.50e+00 4.44e-01 4.40e+02 angle pdb=" O2' A 12439 " pdb=" C2' A 12439 " pdb=" C1' A 12439 " ideal model delta sigma weight residual 111.80 86.40 25.40 1.50e+00 4.44e-01 2.87e+02 angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C4 OMG 12251 " ideal model delta sigma weight residual 108.29 158.99 -50.70 3.00e+00 1.11e-01 2.86e+02 angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C8 OMG 12251 " ideal model delta sigma weight residual 142.82 93.72 49.10 3.00e+00 1.11e-01 2.68e+02 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 143.79 -48.83 3.00e+00 1.11e-01 2.65e+02 ... (remaining 255228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 95523 35.88 - 71.75: 12027 71.75 - 107.63: 1464 107.63 - 143.50: 43 143.50 - 179.38: 41 Dihedral angle restraints: 109098 sinusoidal: 91135 harmonic: 17963 Sorted by residual: dihedral pdb=" C LYS g 131 " pdb=" N LYS g 131 " pdb=" CA LYS g 131 " pdb=" CB LYS g 131 " ideal model delta harmonic sigma weight residual -122.60 -151.11 28.51 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" N LYS g 131 " pdb=" C LYS g 131 " pdb=" CA LYS g 131 " pdb=" CB LYS g 131 " ideal model delta harmonic sigma weight residual 122.80 150.40 -27.60 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" C4' U 4 148 " pdb=" C3' U 4 148 " pdb=" C2' U 4 148 " pdb=" C1' U 4 148 " ideal model delta sinusoidal sigma weight residual -35.00 35.23 -70.23 1 8.00e+00 1.56e-02 9.93e+01 ... (remaining 109095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.055: 32525 1.055 - 2.110: 1 2.110 - 3.164: 0 3.164 - 4.219: 0 4.219 - 5.274: 1 Chirality restraints: 32527 Sorted by residual: chirality pdb=" C28 KIR 6 401 " pdb=" C27 KIR 6 401 " pdb=" C29 KIR 6 401 " pdb=" C45 KIR 6 401 " both_signs ideal model delta sigma weight residual False -2.76 2.52 -5.27 2.00e-01 2.50e+01 6.95e+02 chirality pdb=" CA LYS g 131 " pdb=" N LYS g 131 " pdb=" C LYS g 131 " pdb=" CB LYS g 131 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.53e+01 chirality pdb=" C1' A 12439 " pdb=" O4' A 12439 " pdb=" C2' A 12439 " pdb=" N9 A 12439 " both_signs ideal model delta sigma weight residual False 2.44 1.67 0.76 2.00e-01 2.50e+01 1.46e+01 ... (remaining 32524 not shown) Planarity restraints: 13715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12251 " 0.037 2.00e-02 2.50e+03 5.67e-01 7.23e+03 pdb=" C4' OMG 12251 " 0.428 2.00e-02 2.50e+03 pdb=" O4' OMG 12251 " 0.576 2.00e-02 2.50e+03 pdb=" C3' OMG 12251 " -0.587 2.00e-02 2.50e+03 pdb=" O3' OMG 12251 " -0.586 2.00e-02 2.50e+03 pdb=" C2' OMG 12251 " -0.190 2.00e-02 2.50e+03 pdb=" O2' OMG 12251 " 0.936 2.00e-02 2.50e+03 pdb=" C1' OMG 12251 " 0.234 2.00e-02 2.50e+03 pdb=" N9 OMG 12251 " -0.848 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 21407 " -0.033 2.00e-02 2.50e+03 5.66e-01 7.21e+03 pdb=" C4' 5MC 21407 " -0.431 2.00e-02 2.50e+03 pdb=" O4' 5MC 21407 " -0.610 2.00e-02 2.50e+03 pdb=" C3' 5MC 21407 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 5MC 21407 " 0.567 2.00e-02 2.50e+03 pdb=" C2' 5MC 21407 " 0.208 2.00e-02 2.50e+03 pdb=" O2' 5MC 21407 " -0.909 2.00e-02 2.50e+03 pdb=" C1' 5MC 21407 " -0.234 2.00e-02 2.50e+03 pdb=" N1 5MC 21407 " 0.855 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 11939 " 0.803 2.00e-02 2.50e+03 5.51e-01 6.83e+03 pdb=" C4' 5MU 11939 " -0.234 2.00e-02 2.50e+03 pdb=" O4' 5MU 11939 " -0.615 2.00e-02 2.50e+03 pdb=" C3' 5MU 11939 " 0.223 2.00e-02 2.50e+03 pdb=" O3' 5MU 11939 " -0.873 2.00e-02 2.50e+03 pdb=" C2' 5MU 11939 " 0.599 2.00e-02 2.50e+03 pdb=" O2' 5MU 11939 " 0.541 2.00e-02 2.50e+03 pdb=" C1' 5MU 11939 " -0.433 2.00e-02 2.50e+03 pdb=" N1 5MU 11939 " -0.011 2.00e-02 2.50e+03 ... (remaining 13712 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 38 1.82 - 2.59: 2262 2.59 - 3.36: 192784 3.36 - 4.13: 503161 4.13 - 4.90: 722388 Nonbonded interactions: 1420633 Sorted by model distance: nonbonded pdb=" CD GLN R 6 " pdb=" O LYS R 10 " model vdw 1.049 3.270 nonbonded pdb=" O LEU i 161 " pdb=" OE1 GLN i 164 " model vdw 1.116 3.040 nonbonded pdb=" CB ARG E 80 " pdb=" CE2 TYR E 83 " model vdw 1.183 3.740 nonbonded pdb=" NE2 GLN R 6 " pdb=" O LYS R 10 " model vdw 1.242 2.520 nonbonded pdb=" NZ LYS g 73 " pdb=" OD2 ASP g 165 " model vdw 1.261 2.520 ... (remaining 1420628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 20.610 Check model and map are aligned: 1.710 Set scattering table: 1.090 Process input model: 582.810 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.380 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:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 616.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.004 0.281 170620 Z= 0.248 Angle : 0.733 50.698 255233 Z= 0.407 Chirality : 0.046 5.274 32527 Planarity : 0.018 0.567 13715 Dihedral : 23.359 179.378 97515 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.45 % Favored : 93.29 % Rotamer: Outliers : 0.64 % Allowed : 6.31 % Favored : 93.05 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.11), residues: 6199 helix: 1.45 (0.12), residues: 2019 sheet: -0.58 (0.15), residues: 1165 loop : -1.76 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP h 201 HIS 0.054 0.001 HIS e 31 PHE 0.011 0.001 PHE k 8 TYR 0.024 0.001 TYR g 213 ARG 0.010 0.000 ARG b 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1845 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1812 time to evaluate : 6.673 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 154 ILE cc_start: 0.8533 (tp) cc_final: 0.8327 (mm) REVERT: 6 144 GLU cc_start: 0.4948 (mt-10) cc_final: 0.4572 (mm-30) REVERT: 6 207 ASP cc_start: 0.7341 (t0) cc_final: 0.7125 (t0) REVERT: 6 262 ARG cc_start: 0.5530 (mtm-85) cc_final: 0.5129 (ttp80) REVERT: 6 348 GLU cc_start: 0.6287 (mp0) cc_final: 0.5923 (pm20) REVERT: B 72 ASP cc_start: 0.6917 (p0) cc_final: 0.6617 (p0) REVERT: B 97 LYS cc_start: 0.8979 (tttt) cc_final: 0.8691 (mptt) REVERT: B 98 ASP cc_start: 0.7436 (m-30) cc_final: 0.7006 (m-30) REVERT: E 164 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7401 (pp20) REVERT: F 41 VAL cc_start: 0.7250 (OUTLIER) cc_final: 0.7012 (m) REVERT: F 43 VAL cc_start: 0.7928 (t) cc_final: 0.7667 (p) REVERT: F 64 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7495 (tm-30) REVERT: F 69 ARG cc_start: 0.8559 (tmt170) cc_final: 0.8313 (tmm-80) REVERT: F 75 MET cc_start: 0.7971 (mtp) cc_final: 0.7644 (mtm) REVERT: F 137 ASP cc_start: 0.7107 (t0) cc_final: 0.6733 (t0) REVERT: N 110 MET cc_start: 0.7303 (mmm) cc_final: 0.6624 (mmt) REVERT: R 59 ILE cc_start: 0.8151 (mt) cc_final: 0.7882 (mt) REVERT: S 109 ASP cc_start: 0.7663 (p0) cc_final: 0.7010 (p0) REVERT: Y 28 LEU cc_start: 0.8250 (mt) cc_final: 0.7524 (mt) REVERT: g 45 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8425 (mmmt) REVERT: g 104 TRP cc_start: 0.7806 (t-100) cc_final: 0.7282 (t-100) REVERT: h 34 ASP cc_start: 0.8556 (t70) cc_final: 0.8326 (t0) REVERT: h 49 LYS cc_start: 0.7652 (mttp) cc_final: 0.7370 (tptp) REVERT: h 142 MET cc_start: 0.7358 (mmm) cc_final: 0.6856 (ptt) REVERT: i 74 ASN cc_start: 0.8515 (m110) cc_final: 0.8192 (m110) REVERT: i 136 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7593 (tm-30) REVERT: j 65 GLU cc_start: 0.8255 (tp30) cc_final: 0.7364 (tp30) REVERT: k 72 ASP cc_start: 0.7481 (t0) cc_final: 0.7221 (t0) REVERT: l 68 ASN cc_start: 0.6013 (m-40) cc_final: 0.5259 (t0) REVERT: l 71 PRO cc_start: 0.5604 (Cg_endo) cc_final: 0.4241 (Cg_exo) REVERT: m 27 MET cc_start: 0.7649 (ptp) cc_final: 0.6837 (ptp) REVERT: n 25 ASN cc_start: 0.7762 (t0) cc_final: 0.6721 (t0) REVERT: n 34 SER cc_start: 0.8770 (p) cc_final: 0.8443 (p) REVERT: n 50 GLN cc_start: 0.8051 (mt0) cc_final: 0.7846 (tp40) REVERT: o 97 ASP cc_start: 0.6735 (m-30) cc_final: 0.6183 (p0) REVERT: p 56 ARG cc_start: 0.6729 (ptt180) cc_final: 0.6091 (ptt180) REVERT: r 33 ILE cc_start: 0.5269 (mm) cc_final: 0.4782 (mt) REVERT: r 81 MET cc_start: 0.7822 (mtm) cc_final: 0.7317 (ttp) REVERT: t 6 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7249 (tp30) REVERT: u 76 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7789 (ptpt) REVERT: v 39 LYS cc_start: 0.8547 (ptpt) cc_final: 0.8322 (ptpp) REVERT: w 21 ILE cc_start: 0.7378 (tp) cc_final: 0.7133 (tp) REVERT: w 30 LYS cc_start: 0.9142 (ptmm) cc_final: 0.8837 (tppt) REVERT: w 35 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7511 (tm-30) REVERT: w 50 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8306 (ttmt) REVERT: x 17 LYS cc_start: 0.6030 (pttt) cc_final: 0.5792 (pttp) REVERT: z 16 LEU cc_start: 0.8208 (mp) cc_final: 0.7951 (pp) REVERT: z 54 LYS cc_start: 0.6226 (mttt) cc_final: 0.5741 (mttt) outliers start: 33 outliers final: 4 residues processed: 1834 average time/residue: 1.4515 time to fit residues: 4504.0323 Evaluate side-chains 1051 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1046 time to evaluate : 6.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain x residue 67 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 935 optimal weight: 0.0060 chunk 839 optimal weight: 10.0000 chunk 465 optimal weight: 50.0000 chunk 286 optimal weight: 10.0000 chunk 566 optimal weight: 10.0000 chunk 448 optimal weight: 20.0000 chunk 868 optimal weight: 8.9990 chunk 336 optimal weight: 40.0000 chunk 528 optimal weight: 6.9990 chunk 646 optimal weight: 8.9990 chunk 1006 optimal weight: 30.0000 overall best weight: 7.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 148 GLN 6 97 GLN ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 329 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN D 9 GLN D 115 GLN F 22 GLN F 111 HIS F 116 GLN F 143 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS K 3 GLN K 9 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN U 66 GLN U 69 ASN X 6 GLN ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 31 HIS e 43 HIS f 35 GLN g 120 GLN h 185 ASN i 36 GLN i 54 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 ASN ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 46 GLN l 130 ASN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 81 HIS o 15 HIS ** p 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 105 ASN t 37 ASN u 63 GLN ** v 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 HIS w 52 GLN ** y 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 170620 Z= 0.331 Angle : 0.764 40.107 255233 Z= 0.390 Chirality : 0.038 0.485 32527 Planarity : 0.007 0.129 13715 Dihedral : 24.321 179.483 85171 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.19 % Favored : 91.74 % Rotamer: Outliers : 4.19 % Allowed : 14.99 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.10), residues: 6199 helix: 0.80 (0.12), residues: 2007 sheet: -0.69 (0.15), residues: 1181 loop : -1.90 (0.11), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP B 213 HIS 0.011 0.002 HIS k 3 PHE 0.040 0.003 PHE 6 194 TYR 0.031 0.002 TYR Q 32 ARG 0.019 0.001 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1169 time to evaluate : 6.731 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: 5 126 LYS cc_start: 0.6831 (mmmt) cc_final: 0.6218 (tttt) REVERT: 5 154 ILE cc_start: 0.8435 (tp) cc_final: 0.8189 (mm) REVERT: 6 144 GLU cc_start: 0.4907 (mt-10) cc_final: 0.4560 (mm-30) REVERT: 6 351 MET cc_start: 0.5095 (mtm) cc_final: 0.4045 (tmm) REVERT: 6 376 ILE cc_start: 0.6656 (mp) cc_final: 0.6253 (pt) REVERT: A 16 SER cc_start: 0.8538 (t) cc_final: 0.7862 (p) REVERT: B 100 GLU cc_start: 0.5550 (mm-30) cc_final: 0.5286 (mm-30) REVERT: C 139 SER cc_start: 0.8702 (m) cc_final: 0.8443 (t) REVERT: E 50 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6534 (mt) REVERT: E 83 TYR cc_start: 0.7648 (m-10) cc_final: 0.6730 (m-80) REVERT: F 35 ARG cc_start: 0.7703 (tpp80) cc_final: 0.7155 (tpp80) REVERT: F 64 GLN cc_start: 0.8511 (mm-40) cc_final: 0.7722 (tm-30) REVERT: F 69 ARG cc_start: 0.8761 (tmt170) cc_final: 0.8425 (tmm-80) REVERT: F 75 MET cc_start: 0.8118 (mtp) cc_final: 0.7657 (mtp) REVERT: F 172 LYS cc_start: 0.4593 (pttt) cc_final: 0.4285 (mmmt) REVERT: G 2 GLN cc_start: 0.7252 (pt0) cc_final: 0.6937 (mm-40) REVERT: J 98 GLU cc_start: 0.7473 (pm20) cc_final: 0.7216 (pm20) REVERT: M 106 ASP cc_start: 0.6701 (t0) cc_final: 0.6373 (t0) REVERT: g 104 TRP cc_start: 0.7939 (t-100) cc_final: 0.7442 (t-100) REVERT: g 151 ILE cc_start: 0.8569 (pt) cc_final: 0.8211 (mm) REVERT: h 34 ASP cc_start: 0.8518 (t70) cc_final: 0.8302 (t0) REVERT: h 49 LYS cc_start: 0.7696 (mttp) cc_final: 0.7321 (tptp) REVERT: i 5 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5259 (mt) REVERT: i 136 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7471 (tm-30) REVERT: k 5 GLU cc_start: 0.6416 (mm-30) cc_final: 0.5930 (mp0) REVERT: k 25 TYR cc_start: 0.7824 (m-80) cc_final: 0.7468 (m-80) REVERT: k 72 ASP cc_start: 0.7666 (t0) cc_final: 0.7461 (t0) REVERT: l 31 MET cc_start: 0.7344 (tmm) cc_final: 0.6989 (tmm) REVERT: o 63 ASP cc_start: 0.7447 (t0) cc_final: 0.7126 (t0) REVERT: p 15 GLN cc_start: 0.8164 (tp40) cc_final: 0.7652 (tp-100) REVERT: p 76 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7865 (tm-30) REVERT: p 94 GLU cc_start: 0.6103 (mp0) cc_final: 0.5817 (mp0) REVERT: r 33 ILE cc_start: 0.5380 (mm) cc_final: 0.5131 (mt) REVERT: r 72 GLU cc_start: 0.8008 (tp30) cc_final: 0.7342 (tp30) REVERT: r 81 MET cc_start: 0.8100 (mtm) cc_final: 0.7594 (tpt) REVERT: u 32 PHE cc_start: 0.8247 (p90) cc_final: 0.7924 (p90) REVERT: u 76 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7910 (ptpt) REVERT: w 21 ILE cc_start: 0.7172 (tp) cc_final: 0.6888 (tp) REVERT: w 30 LYS cc_start: 0.9216 (ptmm) cc_final: 0.8563 (tppt) REVERT: w 50 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8259 (tttt) REVERT: w 71 THR cc_start: 0.7048 (p) cc_final: 0.6737 (t) REVERT: x 3 ARG cc_start: 0.4397 (mmt90) cc_final: 0.3728 (mpp-170) REVERT: y 29 ARG cc_start: 0.8621 (mtm180) cc_final: 0.7952 (mmm-85) REVERT: y 53 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7448 (tm-30) REVERT: y 55 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: z 13 ASP cc_start: 0.6231 (t0) cc_final: 0.5948 (t70) REVERT: z 31 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7355 (mm-30) REVERT: z 54 LYS cc_start: 0.6215 (mttt) cc_final: 0.5671 (mttt) outliers start: 216 outliers final: 116 residues processed: 1289 average time/residue: 1.3706 time to fit residues: 3082.2047 Evaluate side-chains 1094 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 975 time to evaluate : 6.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 368 MET Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain g residue 86 SER Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 21 ASN Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 79 ILE Chi-restraints excluded: chain p residue 109 ASN Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 77 ILE Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 23 LYS Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 35 GLN Chi-restraints excluded: chain t residue 61 SER Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 41 PHE Chi-restraints excluded: chain x residue 43 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 55 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 559 optimal weight: 7.9990 chunk 312 optimal weight: 20.0000 chunk 837 optimal weight: 20.0000 chunk 685 optimal weight: 30.0000 chunk 277 optimal weight: 10.0000 chunk 1007 optimal weight: 7.9990 chunk 1088 optimal weight: 30.0000 chunk 897 optimal weight: 9.9990 chunk 999 optimal weight: 8.9990 chunk 343 optimal weight: 30.0000 chunk 808 optimal weight: 6.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 66 HIS 6 97 GLN ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN A 57 HIS B 115 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 9 ASN M 60 GLN N 31 HIS R 6 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN ** b 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 GLN i 116 GLN ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 99 GLN p 101 ASN p 109 ASN ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 77 HIS t 37 ASN ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN w 52 GLN w 54 GLN ** x 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 HIS y 82 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 170620 Z= 0.365 Angle : 0.752 39.904 255233 Z= 0.385 Chirality : 0.039 0.432 32527 Planarity : 0.007 0.137 13715 Dihedral : 24.445 179.867 85169 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.50 % Favored : 91.45 % Rotamer: Outliers : 5.36 % Allowed : 17.56 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.38 (0.10), residues: 6199 helix: 0.51 (0.12), residues: 2028 sheet: -0.86 (0.15), residues: 1184 loop : -1.98 (0.11), residues: 2987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP l 103 HIS 0.013 0.002 HIS L 35 PHE 0.024 0.002 PHE G 46 TYR 0.045 0.002 TYR i 75 ARG 0.012 0.001 ARG S 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1039 time to evaluate : 6.784 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: 6 276 VAL cc_start: 0.6518 (OUTLIER) cc_final: 0.6223 (m) REVERT: 6 329 GLN cc_start: 0.5699 (OUTLIER) cc_final: 0.5278 (mm110) REVERT: 6 376 ILE cc_start: 0.6560 (mp) cc_final: 0.6199 (pt) REVERT: A 16 SER cc_start: 0.8363 (t) cc_final: 0.7937 (p) REVERT: C 139 SER cc_start: 0.8704 (m) cc_final: 0.8463 (t) REVERT: E 46 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6665 (p0) REVERT: E 49 LEU cc_start: 0.5442 (OUTLIER) cc_final: 0.4978 (mt) REVERT: E 50 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6561 (mt) REVERT: E 83 TYR cc_start: 0.7310 (m-10) cc_final: 0.6616 (m-80) REVERT: F 69 ARG cc_start: 0.8883 (tmt170) cc_final: 0.8401 (tmm-80) REVERT: F 163 ARG cc_start: 0.7327 (ptp-170) cc_final: 0.7097 (ptp-170) REVERT: G 2 GLN cc_start: 0.7257 (pt0) cc_final: 0.6983 (mm-40) REVERT: G 46 PHE cc_start: 0.8308 (t80) cc_final: 0.8059 (t80) REVERT: H 52 MET cc_start: 0.0762 (mtt) cc_final: -0.1498 (mmm) REVERT: I 116 MET cc_start: 0.0559 (tpt) cc_final: 0.0181 (tpt) REVERT: U 37 GLU cc_start: 0.7941 (pm20) cc_final: 0.7532 (pm20) REVERT: V 58 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7931 (t) REVERT: f 34 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8656 (ttmt) REVERT: g 100 MET cc_start: 0.7550 (tmm) cc_final: 0.7349 (ppp) REVERT: g 104 TRP cc_start: 0.8045 (t-100) cc_final: 0.7612 (t-100) REVERT: g 168 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6966 (t-170) REVERT: h 34 ASP cc_start: 0.8475 (t70) cc_final: 0.8270 (t0) REVERT: h 49 LYS cc_start: 0.7692 (mttp) cc_final: 0.7285 (tptp) REVERT: h 129 MET cc_start: 0.7714 (mpp) cc_final: 0.7443 (mpp) REVERT: h 134 MET cc_start: 0.8679 (ttp) cc_final: 0.8343 (ttp) REVERT: i 5 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5183 (mt) REVERT: i 124 MET cc_start: 0.7449 (tpp) cc_final: 0.7239 (ttm) REVERT: i 136 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7346 (tm-30) REVERT: j 65 GLU cc_start: 0.8352 (tp30) cc_final: 0.7467 (tp30) REVERT: j 122 ASN cc_start: 0.6484 (OUTLIER) cc_final: 0.5224 (p0) REVERT: k 5 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6160 (mp0) REVERT: k 69 GLU cc_start: 0.8676 (pm20) cc_final: 0.8386 (pm20) REVERT: k 72 ASP cc_start: 0.7662 (t0) cc_final: 0.7433 (t0) REVERT: k 79 ARG cc_start: 0.7705 (ttp-110) cc_final: 0.7408 (ptp90) REVERT: n 46 MET cc_start: 0.7285 (tpt) cc_final: 0.7045 (tpt) REVERT: n 50 GLN cc_start: 0.8083 (mt0) cc_final: 0.7565 (tm-30) REVERT: n 103 PHE cc_start: 0.6475 (m-10) cc_final: 0.5465 (m-80) REVERT: o 17 LEU cc_start: 0.8201 (tp) cc_final: 0.7922 (tp) REVERT: o 63 ASP cc_start: 0.7380 (t0) cc_final: 0.7101 (t70) REVERT: o 65 TYR cc_start: 0.7364 (m-10) cc_final: 0.7040 (m-10) REVERT: q 90 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7709 (mm) REVERT: r 72 GLU cc_start: 0.7758 (tp30) cc_final: 0.6868 (tp30) REVERT: r 81 MET cc_start: 0.7984 (mtm) cc_final: 0.7461 (ttp) REVERT: v 17 MET cc_start: 0.6844 (tmm) cc_final: 0.6278 (ttt) REVERT: w 21 ILE cc_start: 0.7292 (tp) cc_final: 0.7084 (tp) REVERT: w 30 LYS cc_start: 0.9326 (ptmm) cc_final: 0.8590 (tppt) REVERT: w 50 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8481 (tttt) REVERT: w 71 THR cc_start: 0.7019 (p) cc_final: 0.6697 (t) REVERT: x 3 ARG cc_start: 0.4133 (mmt90) cc_final: 0.3470 (mpp-170) REVERT: y 29 ARG cc_start: 0.8628 (mtm180) cc_final: 0.8191 (mmm-85) REVERT: y 55 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: z 13 ASP cc_start: 0.6146 (t0) cc_final: 0.5831 (t70) REVERT: z 54 LYS cc_start: 0.6327 (mttt) cc_final: 0.5747 (mttt) outliers start: 276 outliers final: 168 residues processed: 1210 average time/residue: 1.3074 time to fit residues: 2766.4583 Evaluate side-chains 1105 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 926 time to evaluate : 6.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 ILE Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 158 SER Chi-restraints excluded: chain 6 residue 217 VAL Chi-restraints excluded: chain 6 residue 276 VAL Chi-restraints excluded: chain 6 residue 323 PHE Chi-restraints excluded: chain 6 residue 329 GLN Chi-restraints excluded: chain 6 residue 368 MET Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 37 ARG Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 30 GLU Chi-restraints excluded: chain g residue 49 MET Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 51 TYR Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain j residue 122 ASN Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 29 ILE Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 58 ASN Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 109 ASN Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 38 TYR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 77 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 23 LYS Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 12 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 71 VAL Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 43 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain y residue 82 GLN Chi-restraints excluded: chain z residue 33 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 995 optimal weight: 20.0000 chunk 757 optimal weight: 0.9980 chunk 523 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 481 optimal weight: 50.0000 chunk 676 optimal weight: 30.0000 chunk 1011 optimal weight: 9.9990 chunk 1070 optimal weight: 20.0000 chunk 528 optimal weight: 7.9990 chunk 958 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 GLN ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 52 GLN w 54 GLN ** x 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 170620 Z= 0.268 Angle : 0.688 39.873 255233 Z= 0.357 Chirality : 0.036 0.435 32527 Planarity : 0.006 0.129 13715 Dihedral : 24.381 179.662 85168 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.50 % Favored : 91.43 % Rotamer: Outliers : 5.22 % Allowed : 19.11 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.28 (0.11), residues: 6199 helix: 0.59 (0.12), residues: 2033 sheet: -0.82 (0.15), residues: 1175 loop : -1.91 (0.11), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP l 103 HIS 0.009 0.001 HIS L 35 PHE 0.021 0.002 PHE h 130 TYR 0.032 0.002 TYR D 35 ARG 0.010 0.001 ARG n 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1013 time to evaluate : 6.745 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: 6 265 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4496 (mm) REVERT: 6 276 VAL cc_start: 0.6409 (OUTLIER) cc_final: 0.6100 (m) REVERT: 6 329 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.5257 (mm110) REVERT: 6 376 ILE cc_start: 0.6623 (mp) cc_final: 0.6237 (pt) REVERT: A 16 SER cc_start: 0.8324 (t) cc_final: 0.7933 (p) REVERT: C 139 SER cc_start: 0.8676 (m) cc_final: 0.8468 (t) REVERT: E 44 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5755 (tp) REVERT: E 49 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4852 (mt) REVERT: E 50 LEU cc_start: 0.7252 (mt) cc_final: 0.6582 (mt) REVERT: E 83 TYR cc_start: 0.7237 (m-10) cc_final: 0.6662 (m-80) REVERT: E 158 THR cc_start: 0.7360 (OUTLIER) cc_final: 0.7128 (t) REVERT: F 69 ARG cc_start: 0.8826 (tmt170) cc_final: 0.8163 (ptt-90) REVERT: F 75 MET cc_start: 0.8076 (mtp) cc_final: 0.7716 (mtm) REVERT: G 2 GLN cc_start: 0.7330 (pt0) cc_final: 0.7074 (mm-40) REVERT: I 116 MET cc_start: 0.0681 (tpt) cc_final: 0.0287 (tpt) REVERT: I 135 MET cc_start: -0.0623 (mmm) cc_final: -0.1064 (mmm) REVERT: V 58 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7925 (t) REVERT: e 49 MET cc_start: 0.7311 (mmm) cc_final: 0.7052 (mmm) REVERT: f 34 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8660 (ttmt) REVERT: g 104 TRP cc_start: 0.7962 (t-100) cc_final: 0.7554 (t-100) REVERT: g 151 ILE cc_start: 0.8488 (pt) cc_final: 0.8116 (mm) REVERT: h 49 LYS cc_start: 0.7699 (mttp) cc_final: 0.7282 (tptp) REVERT: h 139 GLN cc_start: 0.7569 (pt0) cc_final: 0.7348 (pp30) REVERT: i 5 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5224 (mt) REVERT: i 74 ASN cc_start: 0.8522 (m110) cc_final: 0.7889 (m-40) REVERT: i 77 LYS cc_start: 0.8448 (mttt) cc_final: 0.8167 (ptpt) REVERT: i 93 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8352 (pp) REVERT: i 124 MET cc_start: 0.7495 (tpp) cc_final: 0.7239 (ttm) REVERT: i 136 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7408 (tm-30) REVERT: j 54 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7714 (tpp80) REVERT: k 5 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6148 (mp0) REVERT: k 25 TYR cc_start: 0.7848 (m-80) cc_final: 0.7458 (m-80) REVERT: k 72 ASP cc_start: 0.7456 (t0) cc_final: 0.7227 (t0) REVERT: k 79 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.7123 (ptp90) REVERT: o 66 GLU cc_start: 0.7983 (pt0) cc_final: 0.7728 (pt0) REVERT: o 71 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.5269 (mm) REVERT: p 40 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7501 (t0) REVERT: p 110 ILE cc_start: 0.8566 (mm) cc_final: 0.8149 (mm) REVERT: q 90 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7840 (mm) REVERT: r 25 VAL cc_start: 0.7488 (OUTLIER) cc_final: 0.7255 (p) REVERT: r 81 MET cc_start: 0.8003 (mtm) cc_final: 0.7553 (tpt) REVERT: s 60 GLN cc_start: 0.7117 (mm-40) cc_final: 0.6902 (mt0) REVERT: u 14 ARG cc_start: 0.8161 (ttt180) cc_final: 0.7698 (tpp80) REVERT: u 54 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7158 (tp) REVERT: v 17 MET cc_start: 0.7149 (tmm) cc_final: 0.6539 (ttt) REVERT: v 28 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.6595 (t80) REVERT: w 71 THR cc_start: 0.7212 (p) cc_final: 0.6899 (t) REVERT: x 3 ARG cc_start: 0.4055 (mmt90) cc_final: 0.3198 (mpp-170) REVERT: y 10 ARG cc_start: 0.6853 (ttm-80) cc_final: 0.6577 (ttm-80) REVERT: y 29 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8024 (mmm-85) REVERT: y 55 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: z 13 ASP cc_start: 0.6128 (t0) cc_final: 0.5753 (t70) REVERT: z 34 ARG cc_start: 0.8386 (tmm-80) cc_final: 0.8172 (tmm-80) REVERT: z 54 LYS cc_start: 0.6370 (mttt) cc_final: 0.5808 (mttt) outliers start: 269 outliers final: 181 residues processed: 1180 average time/residue: 1.3025 time to fit residues: 2691.9811 Evaluate side-chains 1116 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 918 time to evaluate : 6.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 99 SER Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 ILE Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 158 SER Chi-restraints excluded: chain 6 residue 220 ILE Chi-restraints excluded: chain 6 residue 265 LEU Chi-restraints excluded: chain 6 residue 276 VAL Chi-restraints excluded: chain 6 residue 323 PHE Chi-restraints excluded: chain 6 residue 329 GLN Chi-restraints excluded: chain 6 residue 368 MET Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 51 TYR Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 21 ASN Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 58 ASN Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain o residue 82 LYS Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 40 ASN Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 90 LEU Chi-restraints excluded: chain r residue 25 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 77 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 23 LYS Chi-restraints excluded: chain s residue 33 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 34 GLU Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 39 LYS Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 43 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 891 optimal weight: 9.9990 chunk 607 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 797 optimal weight: 6.9990 chunk 441 optimal weight: 10.0000 chunk 913 optimal weight: 5.9990 chunk 740 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 546 optimal weight: 40.0000 chunk 961 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 97 GLN ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 115 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN ** X 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 9 GLN n 50 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 15 GLN ** p 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 GLN ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 52 GLN w 54 GLN ** x 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 170620 Z= 0.351 Angle : 0.744 39.760 255233 Z= 0.383 Chirality : 0.038 0.389 32527 Planarity : 0.006 0.135 13715 Dihedral : 24.455 179.834 85168 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.34 % Favored : 90.60 % Rotamer: Outliers : 6.29 % Allowed : 19.60 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.10), residues: 6199 helix: 0.44 (0.12), residues: 2022 sheet: -0.96 (0.15), residues: 1188 loop : -1.93 (0.11), residues: 2989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP l 103 HIS 0.010 0.002 HIS L 35 PHE 0.022 0.002 PHE E 122 TYR 0.048 0.002 TYR e 64 ARG 0.012 0.001 ARG n 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 979 time to evaluate : 6.779 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: 5 86 ARG cc_start: 0.4010 (tpt-90) cc_final: 0.3736 (ttt90) REVERT: 6 329 GLN cc_start: 0.5684 (OUTLIER) cc_final: 0.5192 (mm110) REVERT: 6 372 LEU cc_start: 0.4761 (OUTLIER) cc_final: 0.4128 (tt) REVERT: 6 376 ILE cc_start: 0.6541 (mp) cc_final: 0.6185 (pt) REVERT: A 16 SER cc_start: 0.8372 (t) cc_final: 0.7935 (p) REVERT: B 77 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8747 (p) REVERT: C 139 SER cc_start: 0.8729 (m) cc_final: 0.8483 (t) REVERT: E 49 LEU cc_start: 0.5561 (OUTLIER) cc_final: 0.5151 (mt) REVERT: E 50 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6602 (mt) REVERT: E 83 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: E 158 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7047 (t) REVERT: F 64 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7737 (mp10) REVERT: F 69 ARG cc_start: 0.8856 (tmt170) cc_final: 0.8326 (tmm-80) REVERT: F 177 LYS cc_start: 0.1365 (OUTLIER) cc_final: 0.1016 (ttpp) REVERT: G 2 GLN cc_start: 0.7383 (pt0) cc_final: 0.7073 (mm-40) REVERT: G 19 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8427 (t) REVERT: H 23 LEU cc_start: 0.2667 (OUTLIER) cc_final: 0.2344 (mt) REVERT: H 52 MET cc_start: 0.0977 (mtt) cc_final: -0.1737 (mmm) REVERT: I 116 MET cc_start: 0.0756 (tpt) cc_final: 0.0331 (tpt) REVERT: J 98 GLU cc_start: 0.7587 (pm20) cc_final: 0.7224 (pm20) REVERT: V 58 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7911 (t) REVERT: V 71 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7986 (ptpp) REVERT: f 36 ARG cc_start: 0.8121 (ttp-170) cc_final: 0.7914 (ttp-170) REVERT: g 104 TRP cc_start: 0.8008 (t-100) cc_final: 0.7637 (t-100) REVERT: g 168 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.6849 (t-170) REVERT: h 49 LYS cc_start: 0.7739 (mttp) cc_final: 0.7345 (tptp) REVERT: i 5 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5197 (mt) REVERT: i 74 ASN cc_start: 0.8550 (m110) cc_final: 0.8101 (m110) REVERT: i 77 LYS cc_start: 0.8371 (mttt) cc_final: 0.8112 (mttt) REVERT: i 178 MET cc_start: 0.1393 (mtp) cc_final: 0.0843 (mtt) REVERT: j 54 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7783 (tpp80) REVERT: j 95 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7504 (t80) REVERT: k 25 TYR cc_start: 0.7980 (m-80) cc_final: 0.7667 (m-80) REVERT: k 35 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7349 (ttmm) REVERT: k 64 VAL cc_start: 0.8603 (t) cc_final: 0.8372 (p) REVERT: k 72 ASP cc_start: 0.7474 (t0) cc_final: 0.7207 (t0) REVERT: l 31 MET cc_start: 0.7507 (tmm) cc_final: 0.6758 (tmm) REVERT: m 5 ASP cc_start: 0.7702 (t0) cc_final: 0.7231 (t0) REVERT: o 71 LEU cc_start: 0.6862 (mm) cc_final: 0.6305 (mm) REVERT: u 14 ARG cc_start: 0.8234 (ttt180) cc_final: 0.7905 (tpp80) REVERT: u 54 LEU cc_start: 0.7721 (mm) cc_final: 0.7181 (tp) REVERT: v 17 MET cc_start: 0.7201 (tmm) cc_final: 0.6584 (ttt) REVERT: v 28 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.6671 (t80) REVERT: v 49 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6717 (tp30) REVERT: w 53 ARG cc_start: 0.8435 (mtm110) cc_final: 0.7822 (ptt180) REVERT: w 71 THR cc_start: 0.7043 (p) cc_final: 0.6727 (t) REVERT: x 41 PHE cc_start: 0.4251 (OUTLIER) cc_final: 0.3900 (p90) REVERT: x 56 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6376 (pp30) REVERT: y 29 ARG cc_start: 0.8623 (mtm180) cc_final: 0.8199 (mmm-85) REVERT: y 55 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: z 13 ASP cc_start: 0.6272 (t0) cc_final: 0.5866 (t70) REVERT: z 54 LYS cc_start: 0.6412 (mttt) cc_final: 0.5860 (mttt) outliers start: 324 outliers final: 212 residues processed: 1179 average time/residue: 1.3037 time to fit residues: 2703.2401 Evaluate side-chains 1150 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 918 time to evaluate : 6.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 34 LEU Chi-restraints excluded: chain 5 residue 98 ASP Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 ILE Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 158 SER Chi-restraints excluded: chain 6 residue 217 VAL Chi-restraints excluded: chain 6 residue 323 PHE Chi-restraints excluded: chain 6 residue 329 GLN Chi-restraints excluded: chain 6 residue 368 MET Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 164 TYR Chi-restraints excluded: chain F residue 177 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 51 TYR Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 95 PHE Chi-restraints excluded: chain j residue 122 ASN Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 58 ASN Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 82 LYS Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 23 LYS Chi-restraints excluded: chain s residue 33 ASP Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 12 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 39 LYS Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 41 PHE Chi-restraints excluded: chain x residue 43 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 360 optimal weight: 20.0000 chunk 964 optimal weight: 9.9990 chunk 211 optimal weight: 50.0000 chunk 628 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 chunk 1072 optimal weight: 8.9990 chunk 889 optimal weight: 20.0000 chunk 496 optimal weight: 20.0000 chunk 89 optimal weight: 50.0000 chunk 354 optimal weight: 20.0000 chunk 562 optimal weight: 5.9990 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 79 HIS ** 6 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 GLN D 156 ASN G 11 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 HIS X 32 ASN ** b 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 29 GLN ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 37 ASN ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 31 ASN ** x 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 170620 Z= 0.464 Angle : 0.842 39.582 255233 Z= 0.428 Chirality : 0.043 0.435 32527 Planarity : 0.007 0.139 13715 Dihedral : 24.668 178.707 85168 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.52 % Favored : 89.40 % Rotamer: Outliers : 6.41 % Allowed : 20.61 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.83 (0.10), residues: 6199 helix: 0.08 (0.11), residues: 2016 sheet: -1.21 (0.15), residues: 1125 loop : -2.14 (0.10), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP l 103 HIS 0.012 0.002 HIS L 35 PHE 0.032 0.003 PHE G 46 TYR 0.053 0.003 TYR e 64 ARG 0.015 0.001 ARG n 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 943 time to evaluate : 6.774 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: 5 86 ARG cc_start: 0.4406 (tpt-90) cc_final: 0.3844 (tpt-90) REVERT: 6 329 GLN cc_start: 0.5582 (OUTLIER) cc_final: 0.5022 (mm110) REVERT: 6 372 LEU cc_start: 0.5095 (OUTLIER) cc_final: 0.4883 (tt) REVERT: 6 376 ILE cc_start: 0.6686 (mp) cc_final: 0.6372 (pt) REVERT: A 16 SER cc_start: 0.8463 (t) cc_final: 0.7955 (p) REVERT: C 139 SER cc_start: 0.8760 (m) cc_final: 0.8476 (t) REVERT: D 124 PHE cc_start: 0.8008 (t80) cc_final: 0.7728 (t80) REVERT: E 44 ILE cc_start: 0.5933 (OUTLIER) cc_final: 0.5656 (tp) REVERT: E 49 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.5507 (mt) REVERT: E 50 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6627 (mt) REVERT: E 83 TYR cc_start: 0.7234 (m-10) cc_final: 0.6736 (m-80) REVERT: F 32 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7025 (tm-30) REVERT: F 64 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7790 (mp10) REVERT: F 69 ARG cc_start: 0.8867 (tmt170) cc_final: 0.8180 (ptt180) REVERT: F 177 LYS cc_start: 0.1657 (OUTLIER) cc_final: 0.1212 (ttpp) REVERT: G 19 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8580 (t) REVERT: G 94 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5717 (mp) REVERT: H 23 LEU cc_start: 0.2228 (OUTLIER) cc_final: 0.1878 (mt) REVERT: H 52 MET cc_start: 0.0976 (mtt) cc_final: -0.1804 (mmm) REVERT: I 116 MET cc_start: 0.0799 (tpt) cc_final: 0.0493 (tpt) REVERT: J 98 GLU cc_start: 0.7741 (pm20) cc_final: 0.7474 (pm20) REVERT: K 80 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6327 (t70) REVERT: V 71 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8092 (ptpp) REVERT: g 104 TRP cc_start: 0.8115 (t-100) cc_final: 0.7700 (t-100) REVERT: g 168 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6840 (t-170) REVERT: h 49 LYS cc_start: 0.7809 (mttp) cc_final: 0.7367 (tptp) REVERT: h 134 MET cc_start: 0.9052 (ttp) cc_final: 0.8764 (ttm) REVERT: i 5 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5203 (mt) REVERT: i 40 GLN cc_start: 0.1496 (OUTLIER) cc_final: -0.0497 (mm-40) REVERT: i 71 GLN cc_start: 0.8756 (pm20) cc_final: 0.8388 (pm20) REVERT: i 74 ASN cc_start: 0.8476 (m110) cc_final: 0.7988 (m110) REVERT: i 77 LYS cc_start: 0.8472 (mttt) cc_final: 0.8216 (mttt) REVERT: i 93 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8464 (pp) REVERT: j 54 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7859 (tpp80) REVERT: k 17 GLN cc_start: 0.7841 (mt0) cc_final: 0.7401 (tp40) REVERT: k 23 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8388 (mp0) REVERT: k 25 TYR cc_start: 0.8168 (m-80) cc_final: 0.7782 (m-80) REVERT: k 35 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7492 (ttmm) REVERT: k 72 ASP cc_start: 0.7625 (t0) cc_final: 0.7376 (t0) REVERT: k 90 MET cc_start: 0.7502 (ptp) cc_final: 0.7108 (ptp) REVERT: l 31 MET cc_start: 0.7538 (tmm) cc_final: 0.6526 (tmm) REVERT: m 38 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7775 (t0) REVERT: o 63 ASP cc_start: 0.7409 (t0) cc_final: 0.5046 (t0) REVERT: o 65 TYR cc_start: 0.7608 (m-10) cc_final: 0.6991 (m-10) REVERT: o 71 LEU cc_start: 0.6812 (mm) cc_final: 0.6438 (mm) REVERT: p 40 ASN cc_start: 0.8084 (m-40) cc_final: 0.7803 (m-40) REVERT: q 29 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7933 (mp10) REVERT: r 81 MET cc_start: 0.8150 (mtm) cc_final: 0.7658 (tpp) REVERT: t 15 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: v 28 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.6899 (t80) REVERT: w 71 THR cc_start: 0.7159 (p) cc_final: 0.6818 (t) REVERT: x 3 ARG cc_start: 0.4113 (mmt90) cc_final: 0.3399 (mpp-170) REVERT: y 53 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7444 (tm-30) REVERT: y 55 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: z 40 LYS cc_start: 0.6803 (ttpt) cc_final: 0.6591 (ttmt) outliers start: 330 outliers final: 236 residues processed: 1160 average time/residue: 1.3203 time to fit residues: 2693.6556 Evaluate side-chains 1134 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 877 time to evaluate : 6.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 137 ASP Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 ILE Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 158 SER Chi-restraints excluded: chain 6 residue 191 LEU Chi-restraints excluded: chain 6 residue 217 VAL Chi-restraints excluded: chain 6 residue 238 VAL Chi-restraints excluded: chain 6 residue 242 VAL Chi-restraints excluded: chain 6 residue 329 GLN Chi-restraints excluded: chain 6 residue 368 MET Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 150 ARG Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 177 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 25 THR Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Y residue 4 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 124 LEU Chi-restraints excluded: chain h residue 154 SER Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 51 TYR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 182 PHE Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 90 THR Chi-restraints excluded: chain j residue 122 ASN Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 85 ILE Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 74 GLU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 38 ASN Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 71 VAL Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 58 ASN Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 82 LYS Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 50 SER Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 29 GLN Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 23 LYS Chi-restraints excluded: chain s residue 33 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 12 VAL Chi-restraints excluded: chain t residue 15 PHE Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 34 GLU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 39 LYS Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 21 LYS Chi-restraints excluded: chain x residue 43 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 33 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 1033 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 610 optimal weight: 0.9990 chunk 782 optimal weight: 1.9990 chunk 606 optimal weight: 8.9990 chunk 902 optimal weight: 4.9990 chunk 598 optimal weight: 5.9990 chunk 1067 optimal weight: 7.9990 chunk 668 optimal weight: 9.9990 chunk 651 optimal weight: 6.9990 chunk 493 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 66 HIS ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 329 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 69 ASN V 12 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 185 ASN ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN ** r 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN ** x 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 170620 Z= 0.219 Angle : 0.691 39.835 255233 Z= 0.359 Chirality : 0.035 0.456 32527 Planarity : 0.006 0.128 13715 Dihedral : 24.506 179.881 85168 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.16 % Rotamer: Outliers : 5.03 % Allowed : 22.55 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.48 (0.11), residues: 6199 helix: 0.42 (0.12), residues: 2036 sheet: -1.08 (0.15), residues: 1155 loop : -1.95 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP l 103 HIS 0.007 0.001 HIS L 35 PHE 0.023 0.002 PHE o 13 TYR 0.038 0.002 TYR e 64 ARG 0.010 0.001 ARG n 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 974 time to evaluate : 6.685 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: 5 86 ARG cc_start: 0.4290 (tpt-90) cc_final: 0.3763 (tpt-90) REVERT: 6 376 ILE cc_start: 0.6690 (mp) cc_final: 0.6343 (pt) REVERT: A 16 SER cc_start: 0.8239 (t) cc_final: 0.7862 (p) REVERT: A 44 LYS cc_start: 0.8331 (tptt) cc_final: 0.7935 (tptt) REVERT: C 139 SER cc_start: 0.8698 (m) cc_final: 0.8442 (t) REVERT: E 50 LEU cc_start: 0.7258 (mt) cc_final: 0.6614 (mt) REVERT: E 83 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: E 158 THR cc_start: 0.7554 (OUTLIER) cc_final: 0.7201 (t) REVERT: F 64 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7813 (mp10) REVERT: F 69 ARG cc_start: 0.8795 (tmt170) cc_final: 0.7917 (ptt180) REVERT: F 75 MET cc_start: 0.7952 (mtp) cc_final: 0.7524 (mtm) REVERT: F 177 LYS cc_start: 0.1375 (OUTLIER) cc_final: 0.0944 (ttpp) REVERT: G 87 GLU cc_start: 0.5604 (OUTLIER) cc_final: 0.5251 (pm20) REVERT: H 23 LEU cc_start: 0.2444 (OUTLIER) cc_final: 0.2030 (mt) REVERT: H 52 MET cc_start: 0.0957 (mtt) cc_final: 0.0121 (mtm) REVERT: I 135 MET cc_start: -0.0906 (mmm) cc_final: -0.1325 (mmm) REVERT: J 98 GLU cc_start: 0.7645 (pm20) cc_final: 0.7441 (pm20) REVERT: U 6 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6439 (mpp80) REVERT: V 71 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7922 (ptpp) REVERT: f 36 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7380 (mtp180) REVERT: g 104 TRP cc_start: 0.7958 (t-100) cc_final: 0.7615 (t-100) REVERT: g 168 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6716 (t-170) REVERT: h 49 LYS cc_start: 0.7716 (mttp) cc_final: 0.7342 (tptp) REVERT: i 5 LEU cc_start: 0.5831 (OUTLIER) cc_final: 0.5284 (mt) REVERT: i 40 GLN cc_start: 0.1345 (OUTLIER) cc_final: -0.0551 (mm-40) REVERT: i 71 GLN cc_start: 0.8600 (pm20) cc_final: 0.8184 (pm20) REVERT: i 74 ASN cc_start: 0.8439 (m110) cc_final: 0.8009 (m110) REVERT: i 77 LYS cc_start: 0.8448 (mttt) cc_final: 0.8246 (mttt) REVERT: i 93 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8409 (pp) REVERT: j 54 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7802 (tpp80) REVERT: k 25 TYR cc_start: 0.8166 (m-80) cc_final: 0.7878 (m-80) REVERT: k 35 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7372 (ttmm) REVERT: k 72 ASP cc_start: 0.7573 (t0) cc_final: 0.7366 (t0) REVERT: l 31 MET cc_start: 0.7412 (tmm) cc_final: 0.6456 (tmm) REVERT: m 5 ASP cc_start: 0.7781 (t0) cc_final: 0.7303 (t0) REVERT: m 94 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7952 (mtmm) REVERT: n 46 MET cc_start: 0.7386 (tpt) cc_final: 0.6834 (tpt) REVERT: n 57 MET cc_start: 0.5377 (tmm) cc_final: 0.5085 (tmm) REVERT: n 115 LYS cc_start: 0.7462 (mttt) cc_final: 0.7245 (mttt) REVERT: o 63 ASP cc_start: 0.7351 (t0) cc_final: 0.5319 (t0) REVERT: o 65 TYR cc_start: 0.7287 (m-10) cc_final: 0.6998 (m-10) REVERT: r 75 MET cc_start: 0.7982 (ppp) cc_final: 0.7768 (ppp) REVERT: r 81 MET cc_start: 0.7943 (mtm) cc_final: 0.7491 (tpt) REVERT: t 15 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: u 54 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7246 (tp) REVERT: u 56 ARG cc_start: 0.8467 (mmm160) cc_final: 0.8164 (mmm160) REVERT: v 17 MET cc_start: 0.7339 (tmm) cc_final: 0.6428 (tmm) REVERT: v 28 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6763 (t80) REVERT: w 53 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7908 (ptp90) REVERT: w 71 THR cc_start: 0.7289 (p) cc_final: 0.6996 (t) REVERT: x 3 ARG cc_start: 0.3720 (mmt90) cc_final: 0.3211 (mpp-170) REVERT: x 56 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.5799 (pp30) REVERT: y 55 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: z 54 LYS cc_start: 0.6502 (mttm) cc_final: 0.6055 (mttt) outliers start: 259 outliers final: 180 residues processed: 1137 average time/residue: 1.3120 time to fit residues: 2625.8353 Evaluate side-chains 1111 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 912 time to evaluate : 6.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 ILE Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 158 SER Chi-restraints excluded: chain 6 residue 238 VAL Chi-restraints excluded: chain 6 residue 323 PHE Chi-restraints excluded: chain 6 residue 351 MET Chi-restraints excluded: chain 6 residue 368 MET Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 177 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 39 TRP Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 51 TYR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 49 PHE Chi-restraints excluded: chain o residue 58 ASN Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 82 LYS Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 96 THR Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 23 LYS Chi-restraints excluded: chain s residue 33 ASP Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 15 PHE Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 54 LEU Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 39 LYS Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 68 LEU Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 43 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 12 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 660 optimal weight: 30.0000 chunk 426 optimal weight: 30.0000 chunk 637 optimal weight: 30.0000 chunk 321 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 678 optimal weight: 40.0000 chunk 727 optimal weight: 7.9990 chunk 527 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 839 optimal weight: 7.9990 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 66 HIS ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 ASN ** P 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN q 77 HIS ** r 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 170620 Z= 0.395 Angle : 0.787 39.647 255233 Z= 0.402 Chirality : 0.040 0.459 32527 Planarity : 0.007 0.136 13715 Dihedral : 24.557 179.301 85167 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.49 % Favored : 89.45 % Rotamer: Outliers : 5.52 % Allowed : 22.43 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.65 (0.10), residues: 6199 helix: 0.30 (0.12), residues: 1998 sheet: -1.16 (0.15), residues: 1184 loop : -2.06 (0.11), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP l 103 HIS 0.010 0.002 HIS L 35 PHE 0.033 0.002 PHE E 177 TYR 0.027 0.002 TYR D 35 ARG 0.013 0.001 ARG n 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 920 time to evaluate : 9.163 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: 5 86 ARG cc_start: 0.4422 (tpt-90) cc_final: 0.3855 (tpt-90) REVERT: 6 376 ILE cc_start: 0.6690 (mp) cc_final: 0.6359 (pt) REVERT: A 16 SER cc_start: 0.8422 (t) cc_final: 0.7962 (p) REVERT: C 94 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: C 139 SER cc_start: 0.8750 (m) cc_final: 0.8465 (t) REVERT: E 38 MET cc_start: 0.5838 (mpp) cc_final: 0.5614 (mpp) REVERT: E 44 ILE cc_start: 0.5714 (OUTLIER) cc_final: 0.5417 (tp) REVERT: E 50 LEU cc_start: 0.7340 (mt) cc_final: 0.6654 (mt) REVERT: E 83 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: E 152 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7214 (mt) REVERT: E 158 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7152 (t) REVERT: F 32 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7014 (tm-30) REVERT: F 64 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7827 (mp10) REVERT: F 69 ARG cc_start: 0.8828 (tmt170) cc_final: 0.8287 (ptt180) REVERT: F 177 LYS cc_start: 0.1441 (OUTLIER) cc_final: 0.0849 (ttpp) REVERT: G 87 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.5111 (pm20) REVERT: H 23 LEU cc_start: 0.2224 (OUTLIER) cc_final: 0.1846 (mt) REVERT: H 52 MET cc_start: 0.0951 (mtt) cc_final: -0.0914 (mmm) REVERT: I 116 MET cc_start: -0.0268 (tpt) cc_final: -0.0546 (tpt) REVERT: I 135 MET cc_start: -0.0684 (mmm) cc_final: -0.1347 (mmm) REVERT: J 98 GLU cc_start: 0.7753 (pm20) cc_final: 0.7416 (pm20) REVERT: P 15 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: U 6 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6390 (mtp85) REVERT: V 71 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7999 (ptpp) REVERT: f 36 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7679 (mtp180) REVERT: g 104 TRP cc_start: 0.8088 (t-100) cc_final: 0.7721 (t-100) REVERT: g 168 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.6825 (t-170) REVERT: h 49 LYS cc_start: 0.7747 (mttp) cc_final: 0.7339 (tptp) REVERT: i 5 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5249 (mt) REVERT: i 71 GLN cc_start: 0.8732 (pm20) cc_final: 0.8525 (pm20) REVERT: i 74 ASN cc_start: 0.8485 (m110) cc_final: 0.8035 (m110) REVERT: i 77 LYS cc_start: 0.8506 (mttt) cc_final: 0.8251 (mttt) REVERT: i 93 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8474 (pp) REVERT: j 54 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7610 (tpp80) REVERT: k 25 TYR cc_start: 0.8215 (m-80) cc_final: 0.7899 (m-80) REVERT: k 35 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7516 (ttmm) REVERT: k 72 ASP cc_start: 0.7652 (t0) cc_final: 0.7436 (t0) REVERT: l 31 MET cc_start: 0.7511 (tmm) cc_final: 0.6554 (tmm) REVERT: m 5 ASP cc_start: 0.7918 (t0) cc_final: 0.7526 (t0) REVERT: m 94 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7886 (mtmm) REVERT: n 115 LYS cc_start: 0.7561 (mttt) cc_final: 0.7331 (mttt) REVERT: o 63 ASP cc_start: 0.7413 (t0) cc_final: 0.5300 (t0) REVERT: o 65 TYR cc_start: 0.7527 (m-10) cc_final: 0.7003 (m-10) REVERT: p 24 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7881 (t-90) REVERT: r 81 MET cc_start: 0.8060 (mtm) cc_final: 0.7609 (tpp) REVERT: t 15 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: u 56 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8063 (mmm160) REVERT: v 17 MET cc_start: 0.7621 (tmm) cc_final: 0.6634 (tmm) REVERT: v 28 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.6837 (t80) REVERT: w 71 THR cc_start: 0.7226 (p) cc_final: 0.6909 (t) REVERT: x 56 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.5719 (pp30) REVERT: z 54 LYS cc_start: 0.6437 (mttm) cc_final: 0.5955 (mttt) outliers start: 284 outliers final: 224 residues processed: 1109 average time/residue: 1.2960 time to fit residues: 2530.9139 Evaluate side-chains 1133 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 888 time to evaluate : 6.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 ILE Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 158 SER Chi-restraints excluded: chain 6 residue 191 LEU Chi-restraints excluded: chain 6 residue 217 VAL Chi-restraints excluded: chain 6 residue 238 VAL Chi-restraints excluded: chain 6 residue 242 VAL Chi-restraints excluded: chain 6 residue 323 PHE Chi-restraints excluded: chain 6 residue 351 MET Chi-restraints excluded: chain 6 residue 368 MET Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 164 TYR Chi-restraints excluded: chain F residue 177 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 96 PHE Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 51 TYR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 140 ASN Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 122 ASN Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 144 LEU Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 74 GLU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 14 ASP Chi-restraints excluded: chain o residue 27 GLU Chi-restraints excluded: chain o residue 49 PHE Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 58 ASN Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain o residue 82 LYS Chi-restraints excluded: chain p residue 24 HIS Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 96 THR Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 23 LYS Chi-restraints excluded: chain s residue 33 ASP Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 15 PHE Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain v residue 76 VAL Chi-restraints excluded: chain v residue 80 GLU Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 68 LEU Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 43 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 12 PHE 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: 9.9990 chunk 933 optimal weight: 8.9990 chunk 995 optimal weight: 6.9990 chunk 1022 optimal weight: 9.9990 chunk 598 optimal weight: 2.9990 chunk 433 optimal weight: 20.0000 chunk 781 optimal weight: 1.9990 chunk 305 optimal weight: 30.0000 chunk 899 optimal weight: 10.0000 chunk 941 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** P 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 185 ASN ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN q 29 GLN ** r 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN ** x 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 170620 Z= 0.244 Angle : 0.701 39.835 255233 Z= 0.364 Chirality : 0.036 0.465 32527 Planarity : 0.006 0.128 13715 Dihedral : 24.482 179.628 85167 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.16 % Favored : 90.77 % Rotamer: Outliers : 4.80 % Allowed : 23.25 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.48 (0.11), residues: 6199 helix: 0.44 (0.12), residues: 2022 sheet: -1.10 (0.15), residues: 1147 loop : -1.95 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP l 103 HIS 0.007 0.001 HIS L 35 PHE 0.038 0.002 PHE E 177 TYR 0.018 0.002 TYR R 2 ARG 0.010 0.001 ARG n 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 939 time to evaluate : 6.809 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: 5 86 ARG cc_start: 0.4404 (tpt-90) cc_final: 0.3846 (tpt-90) REVERT: 6 376 ILE cc_start: 0.6696 (mp) cc_final: 0.6371 (pt) REVERT: A 16 SER cc_start: 0.8279 (t) cc_final: 0.7890 (p) REVERT: C 139 SER cc_start: 0.8692 (m) cc_final: 0.8453 (t) REVERT: E 38 MET cc_start: 0.6132 (mpp) cc_final: 0.5807 (mpp) REVERT: E 44 ILE cc_start: 0.5521 (OUTLIER) cc_final: 0.5258 (tp) REVERT: E 50 LEU cc_start: 0.7347 (mt) cc_final: 0.6641 (mt) REVERT: E 83 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: E 152 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7195 (mt) REVERT: E 158 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7277 (t) REVERT: F 64 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7851 (mp10) REVERT: F 69 ARG cc_start: 0.8756 (tmt170) cc_final: 0.8176 (ptt180) REVERT: F 75 MET cc_start: 0.8017 (mtp) cc_final: 0.7724 (mtm) REVERT: F 177 LYS cc_start: 0.1186 (OUTLIER) cc_final: 0.0816 (ttpp) REVERT: G 87 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.5278 (pm20) REVERT: I 116 MET cc_start: -0.0244 (tpt) cc_final: -0.0517 (tpt) REVERT: I 135 MET cc_start: -0.0664 (mmm) cc_final: -0.1274 (mmm) REVERT: J 98 GLU cc_start: 0.7672 (pm20) cc_final: 0.7319 (pm20) REVERT: V 71 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7821 (ptpp) REVERT: f 36 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7751 (mtp180) REVERT: g 104 TRP cc_start: 0.7975 (t-100) cc_final: 0.7633 (t-100) REVERT: g 168 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6766 (t-170) REVERT: h 49 LYS cc_start: 0.7693 (mttp) cc_final: 0.7387 (tptp) REVERT: h 185 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7546 (t0) REVERT: i 5 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5245 (mt) REVERT: i 74 ASN cc_start: 0.8425 (m110) cc_final: 0.7992 (m110) REVERT: i 93 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8452 (pp) REVERT: j 54 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7592 (tpp80) REVERT: k 17 GLN cc_start: 0.7694 (pt0) cc_final: 0.7391 (pm20) REVERT: k 25 TYR cc_start: 0.8138 (m-80) cc_final: 0.7837 (m-80) REVERT: l 31 MET cc_start: 0.7457 (tmm) cc_final: 0.6719 (tmm) REVERT: m 5 ASP cc_start: 0.7698 (t0) cc_final: 0.7320 (t0) REVERT: m 94 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7984 (mtmm) REVERT: n 46 MET cc_start: 0.7468 (tpt) cc_final: 0.6903 (tpt) REVERT: n 115 LYS cc_start: 0.7457 (mttt) cc_final: 0.7214 (mttt) REVERT: o 63 ASP cc_start: 0.7359 (t0) cc_final: 0.5519 (t0) REVERT: o 65 TYR cc_start: 0.7428 (m-10) cc_final: 0.7101 (m-10) REVERT: r 52 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7022 (pt0) REVERT: r 72 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8420 (mm-30) REVERT: r 81 MET cc_start: 0.8032 (mtm) cc_final: 0.7595 (tpt) REVERT: t 15 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: u 54 LEU cc_start: 0.7735 (mm) cc_final: 0.7248 (tp) REVERT: u 56 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8033 (mmm160) REVERT: v 17 MET cc_start: 0.7375 (tmm) cc_final: 0.6480 (tmm) REVERT: v 28 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.6634 (t80) REVERT: w 53 ARG cc_start: 0.8175 (mtm110) cc_final: 0.7903 (ptp90) REVERT: w 71 THR cc_start: 0.7349 (p) cc_final: 0.7063 (t) REVERT: x 56 GLN cc_start: 0.6732 (OUTLIER) cc_final: 0.6038 (pp30) REVERT: y 16 LYS cc_start: 0.8837 (tttt) cc_final: 0.8567 (tptp) REVERT: y 55 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: z 34 ARG cc_start: 0.8423 (tmm-80) cc_final: 0.8211 (tmm-80) REVERT: z 54 LYS cc_start: 0.6511 (mttm) cc_final: 0.6069 (mttt) outliers start: 247 outliers final: 203 residues processed: 1102 average time/residue: 1.2943 time to fit residues: 2504.7392 Evaluate side-chains 1133 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 912 time to evaluate : 6.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 137 ASP Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 ILE Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 158 SER Chi-restraints excluded: chain 6 residue 191 LEU Chi-restraints excluded: chain 6 residue 238 VAL Chi-restraints excluded: chain 6 residue 242 VAL Chi-restraints excluded: chain 6 residue 323 PHE Chi-restraints excluded: chain 6 residue 351 MET Chi-restraints excluded: chain 6 residue 368 MET Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 177 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 51 TYR Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 122 ASN Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 51 VAL Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain m residue 125 ILE Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain o residue 49 PHE Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 58 ASN Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain o residue 82 LYS Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 96 THR Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain r residue 52 GLN Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 23 LYS Chi-restraints excluded: chain s residue 33 ASP Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 15 PHE Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 65 LEU Chi-restraints excluded: chain w residue 68 LEU Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 43 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Chi-restraints excluded: chain z residue 12 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 991 optimal weight: 0.0270 chunk 653 optimal weight: 30.0000 chunk 1052 optimal weight: 7.9990 chunk 642 optimal weight: 3.9990 chunk 499 optimal weight: 10.0000 chunk 731 optimal weight: 9.9990 chunk 1103 optimal weight: 0.9990 chunk 1015 optimal weight: 20.0000 chunk 879 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 678 optimal weight: 5.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN ** b 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 77 HIS ** r 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN ** x 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 170620 Z= 0.202 Angle : 0.676 39.924 255233 Z= 0.352 Chirality : 0.034 0.446 32527 Planarity : 0.006 0.126 13715 Dihedral : 24.386 179.970 85167 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.39 % Favored : 90.56 % Rotamer: Outliers : 4.31 % Allowed : 24.04 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 6199 helix: 0.53 (0.12), residues: 2030 sheet: -1.12 (0.15), residues: 1113 loop : -1.83 (0.11), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP l 103 HIS 0.010 0.001 HIS x 57 PHE 0.044 0.002 PHE E 177 TYR 0.038 0.002 TYR 5 24 ARG 0.009 0.000 ARG n 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 954 time to evaluate : 9.075 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: 5 86 ARG cc_start: 0.4405 (tpt-90) cc_final: 0.3854 (tpt-90) REVERT: 6 376 ILE cc_start: 0.6753 (mp) cc_final: 0.6421 (pt) REVERT: A 16 SER cc_start: 0.8285 (t) cc_final: 0.7913 (p) REVERT: C 139 SER cc_start: 0.8675 (m) cc_final: 0.8471 (t) REVERT: E 38 MET cc_start: 0.6224 (mpp) cc_final: 0.5920 (mpp) REVERT: E 50 LEU cc_start: 0.7393 (mt) cc_final: 0.6682 (mt) REVERT: E 83 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: E 152 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7014 (mt) REVERT: E 158 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7332 (t) REVERT: F 64 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7824 (mp10) REVERT: F 69 ARG cc_start: 0.8739 (tmt170) cc_final: 0.7938 (ptt180) REVERT: F 75 MET cc_start: 0.7894 (mtp) cc_final: 0.7417 (mtm) REVERT: F 115 HIS cc_start: 0.7849 (t-90) cc_final: 0.7491 (t-90) REVERT: F 177 LYS cc_start: 0.1122 (OUTLIER) cc_final: 0.0678 (ttpp) REVERT: G 43 ASN cc_start: 0.8538 (m110) cc_final: 0.8152 (m-40) REVERT: H 52 MET cc_start: 0.0377 (mtt) cc_final: -0.0486 (mtm) REVERT: I 135 MET cc_start: -0.0773 (mmm) cc_final: -0.1202 (mmm) REVERT: U 6 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6496 (mpp80) REVERT: V 12 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6806 (tp40) REVERT: V 71 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7749 (ptpp) REVERT: f 36 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7657 (mtp180) REVERT: g 27 MET cc_start: 0.7457 (mmm) cc_final: 0.6973 (mmm) REVERT: g 104 TRP cc_start: 0.7973 (t-100) cc_final: 0.7656 (t-100) REVERT: g 168 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.6631 (t-170) REVERT: h 49 LYS cc_start: 0.7693 (mttp) cc_final: 0.7384 (tptp) REVERT: i 5 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5291 (mt) REVERT: i 71 GLN cc_start: 0.8470 (pm20) cc_final: 0.8169 (pm20) REVERT: j 32 SER cc_start: 0.9058 (m) cc_final: 0.8810 (t) REVERT: j 54 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7502 (tpp80) REVERT: j 65 GLU cc_start: 0.8329 (tp30) cc_final: 0.7428 (tp30) REVERT: k 25 TYR cc_start: 0.8129 (m-80) cc_final: 0.7811 (m-80) REVERT: l 31 MET cc_start: 0.7368 (tmm) cc_final: 0.6408 (tmm) REVERT: m 5 ASP cc_start: 0.7807 (t0) cc_final: 0.7454 (t0) REVERT: m 94 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7922 (mtmm) REVERT: n 46 MET cc_start: 0.7416 (tpt) cc_final: 0.6834 (tpt) REVERT: n 115 LYS cc_start: 0.7402 (mttt) cc_final: 0.7150 (mttt) REVERT: o 63 ASP cc_start: 0.7414 (t0) cc_final: 0.5836 (t0) REVERT: o 65 TYR cc_start: 0.7400 (m-10) cc_final: 0.7118 (m-10) REVERT: r 75 MET cc_start: 0.8029 (ppp) cc_final: 0.7715 (pmm) REVERT: r 81 MET cc_start: 0.8009 (mtm) cc_final: 0.7644 (tpp) REVERT: t 15 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: u 32 PHE cc_start: 0.8083 (p90) cc_final: 0.7843 (p90) REVERT: u 54 LEU cc_start: 0.7775 (mm) cc_final: 0.7308 (tp) REVERT: u 56 ARG cc_start: 0.8537 (mmm160) cc_final: 0.8008 (mmm160) REVERT: v 17 MET cc_start: 0.7304 (tmm) cc_final: 0.6361 (tmm) REVERT: v 28 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6561 (t80) REVERT: w 53 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7890 (ptp90) REVERT: w 71 THR cc_start: 0.7408 (p) cc_final: 0.7106 (t) REVERT: x 56 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6237 (pp30) REVERT: y 10 ARG cc_start: 0.7185 (ttm-80) cc_final: 0.6808 (ttm-80) REVERT: y 16 LYS cc_start: 0.8830 (tttt) cc_final: 0.8549 (tptp) REVERT: y 29 ARG cc_start: 0.8652 (mtm180) cc_final: 0.7964 (mmm-85) REVERT: y 55 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: z 13 ASP cc_start: 0.6209 (t0) cc_final: 0.5812 (t70) REVERT: z 31 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8008 (mm-30) REVERT: z 54 LYS cc_start: 0.6431 (mttm) cc_final: 0.6007 (mttt) outliers start: 222 outliers final: 184 residues processed: 1094 average time/residue: 1.2995 time to fit residues: 2503.8819 Evaluate side-chains 1116 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 918 time to evaluate : 6.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 137 ASP Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 ILE Chi-restraints excluded: chain 6 residue 127 VAL Chi-restraints excluded: chain 6 residue 158 SER Chi-restraints excluded: chain 6 residue 191 LEU Chi-restraints excluded: chain 6 residue 238 VAL Chi-restraints excluded: chain 6 residue 242 VAL Chi-restraints excluded: chain 6 residue 323 PHE Chi-restraints excluded: chain 6 residue 368 MET Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 177 LYS Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 66 ASN Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 71 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain X residue 5 CYS Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain f residue 16 ILE Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain g residue 85 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 168 HIS Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 56 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 162 ILE Chi-restraints excluded: chain i residue 5 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 40 GLN Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 61 VAL Chi-restraints excluded: chain i residue 142 VAL Chi-restraints excluded: chain i residue 145 ILE Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 122 ASN Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 HIS Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 54 LEU Chi-restraints excluded: chain k residue 92 THR Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 94 LYS Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 35 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 61 LEU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain o residue 10 LEU Chi-restraints excluded: chain o residue 49 PHE Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 60 ASP Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 96 THR Chi-restraints excluded: chain p residue 100 LEU Chi-restraints excluded: chain p residue 114 THR Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain r residue 45 ILE Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain s residue 23 LYS Chi-restraints excluded: chain s residue 33 ASP Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 15 PHE Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 38 ILE Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 65 LEU Chi-restraints excluded: chain w residue 68 LEU Chi-restraints excluded: chain x residue 13 LEU Chi-restraints excluded: chain x residue 14 HIS Chi-restraints excluded: chain x residue 43 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 56 GLN Chi-restraints excluded: chain y residue 30 THR Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain y residue 55 GLN Chi-restraints excluded: chain y residue 75 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 538 optimal weight: 5.9990 chunk 698 optimal weight: 10.0000 chunk 936 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 810 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 880 optimal weight: 30.0000 chunk 368 optimal weight: 20.0000 chunk 904 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN ** b 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 56 GLN ** 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 = 0.3956 r_free = 0.3956 target = 0.086018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057648 restraints weight = 707238.905| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.86 r_work: 0.3031 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.466 170620 Z= 0.312 Angle : 0.702 59.138 255233 Z= 0.369 Chirality : 0.037 0.701 32527 Planarity : 0.006 0.126 13715 Dihedral : 24.383 179.914 85167 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.34 % Favored : 90.61 % Rotamer: Outliers : 4.23 % Allowed : 24.53 % Favored : 71.24 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.37 (0.11), residues: 6199 helix: 0.52 (0.12), residues: 2030 sheet: -1.11 (0.15), residues: 1111 loop : -1.84 (0.11), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP l 103 HIS 0.012 0.001 HIS N 16 PHE 0.139 0.002 PHE F 52 TYR 0.027 0.002 TYR i 76 ARG 0.037 0.001 ARG j 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42779.22 seconds wall clock time: 747 minutes 49.89 seconds (44869.89 seconds total)