Starting phenix.real_space_refine on Fri Mar 22 03:25:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oig_12929/03_2024/7oig_12929_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oig_12929/03_2024/7oig_12929.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oig_12929/03_2024/7oig_12929_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oig_12929/03_2024/7oig_12929_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oig_12929/03_2024/7oig_12929_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oig_12929/03_2024/7oig_12929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oig_12929/03_2024/7oig_12929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oig_12929/03_2024/7oig_12929_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oig_12929/03_2024/7oig_12929_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 2 6.06 5 P 4651 5.49 5 Mg 400 5.21 5 S 150 5.16 5 C 72657 2.51 5 N 26976 2.21 5 O 40300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 37": "NH1" <-> "NH2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K ARG 123": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 25": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O ARG 89": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P ARG 33": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 68": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 6": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 82": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 94": "NH1" <-> "NH2" Residue "U ARG 19": "NH1" <-> "NH2" Residue "V PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 45": "NH1" <-> "NH2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X ARG 47": "NH1" <-> "NH2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 30": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Z ARG 56": "NH1" <-> "NH2" Residue "Z ARG 63": "NH1" <-> "NH2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "b GLU 7": "OE1" <-> "OE2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "c ARG 3": "NH1" <-> "NH2" Residue "c ARG 14": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 41": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 42": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "f ARG 63": "NH1" <-> "NH2" Residue "f ARG 74": "NH1" <-> "NH2" Residue "f GLU 78": "OE1" <-> "OE2" Residue "f ARG 208": "NH1" <-> "NH2" Residue "f ARG 225": "NH1" <-> "NH2" Residue "g ARG 54": "NH1" <-> "NH2" Residue "g ARG 72": "NH1" <-> "NH2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 131": "NH1" <-> "NH2" Residue "g ARG 132": "NH1" <-> "NH2" Residue "g ARG 164": "NH1" <-> "NH2" Residue "h ARG 73": "NH1" <-> "NH2" Residue "h ARG 81": "NH1" <-> "NH2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i ARG 69": "NH1" <-> "NH2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i ARG 157": "NH1" <-> "NH2" Residue "j PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 79": "NH1" <-> "NH2" Residue "k ARG 4": "NH1" <-> "NH2" Residue "k ARG 53": "NH1" <-> "NH2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "k ARG 92": "NH1" <-> "NH2" Residue "l GLU 73": "OE1" <-> "OE2" Residue "l GLU 91": "OE1" <-> "OE2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m ARG 41": "NH1" <-> "NH2" Residue "m ARG 130": "NH1" <-> "NH2" Residue "n ARG 5": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n ARG 89": "NH1" <-> "NH2" Residue "o ARG 37": "NH1" <-> "NH2" Residue "o ARG 69": "NH1" <-> "NH2" Residue "o ARG 93": "NH1" <-> "NH2" Residue "o GLU 94": "OE1" <-> "OE2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 50": "NH1" <-> "NH2" Residue "p ARG 83": "NH1" <-> "NH2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "q ARG 109": "NH1" <-> "NH2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "r ARG 69": "NH1" <-> "NH2" Residue "r ARG 85": "NH1" <-> "NH2" Residue "s ARG 72": "NH1" <-> "NH2" Residue "s ARG 89": "NH1" <-> "NH2" Residue "t ARG 28": "NH1" <-> "NH2" Residue "t ARG 51": "NH1" <-> "NH2" Residue "u ARG 11": "NH1" <-> "NH2" Residue "u ARG 27": "NH1" <-> "NH2" Residue "u ARG 65": "NH1" <-> "NH2" Residue "u ARG 77": "NH1" <-> "NH2" Residue "v ARG 61": "NH1" <-> "NH2" Residue "w ARG 32": "NH1" <-> "NH2" Residue "x ARG 60": "NH1" <-> "NH2" Residue "x ARG 74": "NH1" <-> "NH2" Residue "y ARG 33": "NH1" <-> "NH2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y ARG 55": "NH1" <-> "NH2" Residue "y ARG 62": "NH1" <-> "NH2" Residue "y ARG 67": "NH1" <-> "NH2" Residue "y ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145136 Number of models: 1 Model: "" Number of chains: 68 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 289, 'rna2p_pyr': 166, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 460, 'rna3p': 2442} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 2, 'rna2p_pur': 117, 'rna2p_pyr': 89, 'rna3p': 9, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 207, 'rna3p': 1326} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "4" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "C" 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: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" 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: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "K" 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: "L" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "M" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "T" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "U" 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: "V" 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: "W" 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: "X" 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: "Y" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Z" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" 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: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "c" 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: "d" 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: "e" 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: "f" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "g" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "h" 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: "i" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "j" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "k" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "l" 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: "m" 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: "n" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "o" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "p" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} 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: "q" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "r" 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: "s" 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: "t" 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: "u" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "v" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "w" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "x" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "y" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "z" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1891 Inner-chain residues flagged as termini: ['pdbres=" U z 8 "', 'pdbres=" G z 9 "', 'pdbres=" U z 20 "', 'pdbres=" U z 67 "'] Classifications: {'RNA': 88} Modifications used: {'p5*END': 4, 'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p': 1, 'rna3p_pur': 40, 'rna3p_pyr': 33} Link IDs: {'rna2p': 13, 'rna3p': 74} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 205 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 270 Unusual residues: {' MG': 270} Classifications: {'undetermined': 270} Link IDs: {None: 269} Chain: "2" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Unusual residues: {' MG': 113} Classifications: {'undetermined': 113} Link IDs: {None: 112} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "4" 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: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0GBZ SG CYS Z 16 64.642 60.071 105.534 1.00108.33 S ATOM A0GCB SG CYS Z 18 62.527 58.426 102.204 1.00110.38 S ATOM A0GG9 SG CYS Z 37 65.671 59.152 101.994 1.00106.66 S ATOM A0GGU SG CYS Z 40 64.281 62.046 102.623 1.00108.08 S ATOM A0I1V SG CYS e 11 142.922 116.631 48.063 1.00 86.91 S ATOM A0I2K SG CYS e 14 145.528 114.842 49.512 1.00 83.17 S ATOM A0I5F SG CYS e 27 145.321 118.715 47.949 1.00 84.21 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13142 " occ=0.50 Time building chain proxies: 56.49, per 1000 atoms: 0.39 Number of scatterers: 145136 At special positions: 0 Unit cell: (276.06, 267.5, 232.19, 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 2 29.99 S 150 16.00 P 4651 15.00 Mg 400 11.99 O 40300 8.00 N 26976 7.00 C 72657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 65.16 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Z 101 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 37 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 16 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 40 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 18 " pdb=" ZN e 101 " pdb="ZN ZN e 101 " - pdb=" ND1 HIS e 33 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 14 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 27 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 11 " Number of angles added : 9 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10532 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: 177 helices and 72 sheets defined 39.1% alpha, 20.4% beta 1572 base pairs and 2585 stacking pairs defined. Time for finding SS restraints: 71.70 Creating SS restraints... Processing helix chain 'C' and resid 10 through 16 removed outlier: 7.503A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.004A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.004A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.505A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 4.072A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.985A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.677A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.033A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.651A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.524A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 6.146A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 21 removed outlier: 5.205A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.975A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 47' Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.582A pdb=" N ALA F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.485A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 3.606A pdb=" N VAL F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.437A pdb=" N GLY F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.738A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.813A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 removed outlier: 3.638A pdb=" N GLN G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.715A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 removed outlier: 4.494A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 74 removed outlier: 4.459A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'I' and resid 24 through 38 removed outlier: 4.110A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 4.449A pdb=" N ILE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 123 removed outlier: 3.785A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LYS I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 119 Processing helix chain 'K' and resid 37 through 42 removed outlier: 4.177A pdb=" N ARG K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N SER K 42 " --> pdb=" O GLN K 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 37 through 42' Processing helix chain 'K' and resid 56 through 62 Proline residue: K 62 - end of helix Processing helix chain 'K' and resid 68 through 75 removed outlier: 4.074A pdb=" N ALA K 72 " --> pdb=" O SER K 68 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 85 removed outlier: 4.051A pdb=" N LEU K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 78 through 85' Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 128 through 139 Processing helix chain 'L' and resid 42 through 58 Processing helix chain 'L' and resid 109 through 125 removed outlier: 3.961A pdb=" N LYS L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Proline residue: L 125 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 57 removed outlier: 3.610A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.491A pdb=" N THR M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.652A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 2 through 22 removed outlier: 4.552A pdb=" N ARG N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG N 16 " --> pdb=" O THR N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 4.777A pdb=" N GLN N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 86 Processing helix chain 'N' and resid 101 through 114 Processing helix chain 'O' and resid 2 through 13 removed outlier: 3.641A pdb=" N GLU O 11 " --> pdb=" O GLN O 7 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN O 12 " --> pdb=" O LEU O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 104 removed outlier: 3.821A pdb=" N ARG O 103 " --> pdb=" O TYR O 99 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 99 through 104' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.683A pdb=" N ILE P 17 " --> pdb=" O ARG P 13 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.825A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.907A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG P 58 " --> pdb=" O LYS P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 removed outlier: 3.586A pdb=" N ASN P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 103 through 118 Processing helix chain 'R' and resid 13 through 25 removed outlier: 3.727A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG R 25 " --> pdb=" O ALA R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 3.769A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.827A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS R 70 " --> pdb=" O ILE R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 3 through 11 removed outlier: 4.367A pdb=" N LEU S 11 " --> pdb=" O LEU S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 27 Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'T' and resid 66 through 71 removed outlier: 3.760A pdb=" N VAL T 70 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 66 through 71' Processing helix chain 'U' and resid 13 through 24 Processing helix chain 'U' and resid 43 through 53 removed outlier: 3.572A pdb=" N VAL U 47 " --> pdb=" O ASP U 43 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA U 52 " --> pdb=" O MET U 48 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 59 Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 2 through 10 removed outlier: 3.904A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS X 9 " --> pdb=" O GLU X 5 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 removed outlier: 4.058A pdb=" N GLY X 35 " --> pdb=" O GLN X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 62 removed outlier: 4.262A pdb=" N LYS X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY X 62 " --> pdb=" O ASN X 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 28 Processing helix chain 'Y' and resid 41 through 52 Processing helix chain 'Z' and resid 44 through 51 removed outlier: 5.367A pdb=" N GLN Z 48 " --> pdb=" O PHE Z 44 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL Z 51 " --> pdb=" O LYS Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 65 removed outlier: 4.153A pdb=" N PHE Z 64 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASN Z 65 " --> pdb=" O ASN Z 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 19 removed outlier: 4.808A pdb=" N HIS a 19 " --> pdb=" O MET a 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 16 Processing helix chain 'c' and resid 17 through 25 removed outlier: 4.261A pdb=" N THR c 24 " --> pdb=" O ALA c 20 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS c 25 " --> pdb=" O ARG c 21 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 38 Processing helix chain 'd' and resid 7 through 14 Processing helix chain 'd' and resid 32 through 37 removed outlier: 4.579A pdb=" N LYS d 36 " --> pdb=" O ILE d 32 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA d 37 " --> pdb=" O LEU d 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 32 through 37' Processing helix chain 'd' and resid 38 through 46 Proline residue: d 46 - end of helix Processing helix chain 'd' and resid 51 through 63 removed outlier: 4.706A pdb=" N GLY d 56 " --> pdb=" O LYS d 52 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU d 57 " --> pdb=" O GLY d 53 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL d 58 " --> pdb=" O ASP d 54 " (cutoff:3.500A) Proline residue: d 63 - end of helix Processing helix chain 'f' and resid 5 through 13 Processing helix chain 'f' and resid 42 through 64 Proline residue: f 48 - end of helix Processing helix chain 'f' and resid 73 through 88 removed outlier: 6.364A pdb=" N SER f 77 " --> pdb=" O LYS f 73 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU f 78 " --> pdb=" O ARG f 74 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA f 79 " --> pdb=" O ALA f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 122 removed outlier: 4.486A pdb=" N GLN f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER f 110 " --> pdb=" O THR f 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 130 through 148 Processing helix chain 'f' and resid 165 through 170 Processing helix chain 'f' and resid 171 through 180 Processing helix chain 'f' and resid 192 through 197 removed outlier: 4.781A pdb=" N VAL f 196 " --> pdb=" O ASP f 192 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP f 197 " --> pdb=" O PRO f 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 192 through 197' Processing helix chain 'f' and resid 206 through 227 Processing helix chain 'g' and resid 6 through 12 Processing helix chain 'g' and resid 28 through 48 Processing helix chain 'g' and resid 72 through 78 removed outlier: 4.004A pdb=" N VAL g 76 " --> pdb=" O ARG g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 96 Processing helix chain 'g' and resid 112 through 127 Processing helix chain 'g' and resid 129 through 145 Processing helix chain 'h' and resid 7 through 16 removed outlier: 4.092A pdb=" N LEU h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 27 through 32 Processing helix chain 'h' and resid 49 through 66 Processing helix chain 'h' and resid 68 through 83 removed outlier: 5.204A pdb=" N LYS h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 97 Processing helix chain 'h' and resid 98 through 106 Processing helix chain 'h' and resid 110 through 121 Processing helix chain 'h' and resid 146 through 151 removed outlier: 4.248A pdb=" N LYS h 151 " --> pdb=" O GLU h 147 " (cutoff:3.500A) Processing helix chain 'h' and resid 152 through 166 removed outlier: 3.997A pdb=" N LYS h 156 " --> pdb=" O GLN h 152 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU h 163 " --> pdb=" O LEU h 159 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN h 164 " --> pdb=" O GLU h 160 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 187 through 192 removed outlier: 3.737A pdb=" N LEU h 191 " --> pdb=" O GLU h 187 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER h 192 " --> pdb=" O ARG h 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 187 through 192' Processing helix chain 'h' and resid 196 through 206 removed outlier: 4.084A pdb=" N ILE h 200 " --> pdb=" O ASN h 196 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS h 206 " --> pdb=" O GLU h 202 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 71 removed outlier: 3.605A pdb=" N ARG i 69 " --> pdb=" O GLU i 65 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN i 70 " --> pdb=" O LYS i 66 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET i 71 " --> pdb=" O ALA i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 109 through 119 removed outlier: 3.842A pdb=" N ALA i 113 " --> pdb=" O GLY i 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 147 Processing helix chain 'i' and resid 149 through 158 Processing helix chain 'i' and resid 160 through 165 Processing helix chain 'j' and resid 11 through 16 removed outlier: 3.937A pdb=" N SER j 15 " --> pdb=" O HIS j 11 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU j 16 " --> pdb=" O PRO j 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 11 through 16' Processing helix chain 'j' and resid 17 through 33 Processing helix chain 'j' and resid 67 through 81 removed outlier: 3.633A pdb=" N ILE j 71 " --> pdb=" O PRO j 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 20 through 31 Processing helix chain 'k' and resid 35 through 55 removed outlier: 3.762A pdb=" N ALA k 39 " --> pdb=" O LYS k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 70 removed outlier: 3.687A pdb=" N VAL k 69 " --> pdb=" O ALA k 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 111 Processing helix chain 'k' and resid 115 through 130 Processing helix chain 'k' and resid 132 through 149 Processing helix chain 'l' and resid 5 through 21 Processing helix chain 'l' and resid 30 through 44 Processing helix chain 'l' and resid 112 through 120 Processing helix chain 'm' and resid 34 through 39 Processing helix chain 'm' and resid 41 through 56 removed outlier: 3.610A pdb=" N ARG m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) Proline residue: m 51 - end of helix removed outlier: 4.162A pdb=" N ASP m 56 " --> pdb=" O LEU m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 71 through 92 Processing helix chain 'm' and resid 94 through 102 removed outlier: 4.054A pdb=" N LYS m 100 " --> pdb=" O SER m 96 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 33 removed outlier: 3.818A pdb=" N GLU n 27 " --> pdb=" O ALA n 23 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR n 28 " --> pdb=" O GLU n 24 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA n 29 " --> pdb=" O ILE n 25 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 5.267A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 51 removed outlier: 4.205A pdb=" N GLY o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 59 removed outlier: 4.054A pdb=" N SER o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR o 59 " --> pdb=" O SER o 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 54 through 59' Processing helix chain 'o' and resid 60 through 75 Processing helix chain 'o' and resid 93 through 104 removed outlier: 5.243A pdb=" N ILE o 97 " --> pdb=" O ARG o 93 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 10 Processing helix chain 'p' and resid 113 through 118 removed outlier: 3.894A pdb=" N TYR p 117 " --> pdb=" O ALA p 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 22 removed outlier: 4.306A pdb=" N ILE q 22 " --> pdb=" O ALA q 18 " (cutoff:3.500A) Processing helix chain 'q' and resid 26 through 38 Processing helix chain 'q' and resid 49 through 64 removed outlier: 4.153A pdb=" N PHE q 63 " --> pdb=" O GLU q 59 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL q 64 " --> pdb=" O VAL q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 84 Processing helix chain 'q' and resid 85 through 94 Processing helix chain 'q' and resid 106 through 111 Processing helix chain 'r' and resid 3 through 21 removed outlier: 3.824A pdb=" N PHE r 21 " --> pdb=" O ALA r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 22 through 33 Processing helix chain 'r' and resid 37 through 52 Proline residue: r 52 - end of helix Processing helix chain 'r' and resid 56 through 61 removed outlier: 4.064A pdb=" N GLN r 60 " --> pdb=" O SER r 56 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ARG r 61 " --> pdb=" O PRO r 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 56 through 61' Processing helix chain 'r' and resid 80 through 91 Processing helix chain 's' and resid 4 through 16 Processing helix chain 's' and resid 24 through 43 removed outlier: 4.594A pdb=" N GLY s 41 " --> pdb=" O ASN s 37 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS s 42 " --> pdb=" O HIS s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 49 through 74 removed outlier: 3.874A pdb=" N GLY s 55 " --> pdb=" O HIS s 51 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 86 Processing helix chain 't' and resid 53 through 64 Processing helix chain 't' and resid 68 through 82 Processing helix chain 'v' and resid 11 through 17 Processing helix chain 'v' and resid 25 through 34 removed outlier: 5.660A pdb=" N THR v 34 " --> pdb=" O LYS v 30 " (cutoff:3.500A) Processing helix chain 'v' and resid 41 through 46 removed outlier: 3.712A pdb=" N THR v 45 " --> pdb=" O PRO v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 66 removed outlier: 3.745A pdb=" N ARG v 61 " --> pdb=" O ARG v 57 " (cutoff:3.500A) Processing helix chain 'w' and resid 12 through 26 Processing helix chain 'w' and resid 70 through 76 removed outlier: 4.519A pdb=" N PHE w 74 " --> pdb=" O LYS w 70 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA w 75 " --> pdb=" O LEU w 71 " (cutoff:3.500A) Proline residue: w 76 - end of helix No H-bonds generated for 'chain 'w' and resid 70 through 76' Processing helix chain 'w' and resid 64 through 69 removed outlier: 3.620A pdb=" N VAL w 67 " --> pdb=" O ASP w 64 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY w 68 " --> pdb=" O GLU w 65 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS w 69 " --> pdb=" O MET w 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 64 through 69' Processing helix chain 'x' and resid 4 through 41 Processing helix chain 'x' and resid 44 through 65 Proline residue: x 56 - end of helix Processing helix chain 'x' and resid 68 through 87 removed outlier: 4.868A pdb=" N ALA x 87 " --> pdb=" O ILE x 83 " (cutoff:3.500A) Processing helix chain 'y' and resid 11 through 27 Processing helix chain 'y' and resid 28 through 37 removed outlier: 5.027A pdb=" N PHE y 37 " --> pdb=" O ARG y 33 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 69 removed outlier: 4.202A pdb=" N LYS y 59 " --> pdb=" O ARG y 55 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG y 67 " --> pdb=" O GLU y 63 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR y 68 " --> pdb=" O ASN y 64 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG y 69 " --> pdb=" O ALA y 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 8 Processing helix chain 'B' and resid 9 through 15 removed outlier: 4.360A pdb=" N ASN B 13 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP B 15 " --> pdb=" O TRP B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 9 through 15' Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 6.619A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.385A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.478A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 9 removed outlier: 4.272A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 13.378A pdb=" N GLY D 198 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 11.813A pdb=" N LYS D 114 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 10 through 16 removed outlier: 4.010A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.863A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.728A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.118A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 1 through 6 removed outlier: 4.392A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 117 through 120 Processing sheet with id= 12, first strand: chain 'F' and resid 65 through 69 removed outlier: 4.958A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 16 through 19 removed outlier: 4.008A pdb=" N ASP G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 15, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.020A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 17, first strand: chain 'H' and resid 17 through 20 removed outlier: 4.558A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 76 through 82 removed outlier: 5.331A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 142 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL H 130 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.964A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 74 through 78 removed outlier: 7.152A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 56 through 61 removed outlier: 4.686A pdb=" N ASP J 56 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS J 40 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.744A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 120 through 123 removed outlier: 3.514A pdb=" N LYS K 141 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 122 " --> pdb=" O LYS K 141 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 37 through 40 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.647A pdb=" N TYR L 103 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU L 33 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS L 100 " --> pdb=" O ALA L 35 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 30 through 36 removed outlier: 7.928A pdb=" N SER L 30 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS L 127 " --> pdb=" O VAL L 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.149A pdb=" N ARG M 103 " --> pdb=" O ASN M 107 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE M 113 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE M 97 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU M 115 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 49 through 52 removed outlier: 3.851A pdb=" N VAL N 49 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 38 through 45 removed outlier: 6.643A pdb=" N THR O 25 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.826A pdb=" N ALA O 49 " --> pdb=" O THR O 60 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG O 53 " --> pdb=" O HIS O 56 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N SER O 57 " --> pdb=" O THR O 76 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 11 through 15 removed outlier: 3.673A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN Q 43 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU Q 46 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.660A pdb=" N GLN Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP Q 95 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 34, first strand: chain 'Q' and resid 65 through 77 removed outlier: 5.039A pdb=" N GLN Q 91 " --> pdb=" O GLY Q 69 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS Q 73 " --> pdb=" O GLN Q 87 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN Q 87 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL Q 75 " --> pdb=" O LYS Q 85 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS Q 85 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE Q 77 " --> pdb=" O TYR Q 83 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N TYR Q 83 " --> pdb=" O PHE Q 77 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 36, first strand: chain 'S' and resid 12 through 15 removed outlier: 5.059A pdb=" N VAL S 31 " --> pdb=" O HIS S 15 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASN S 28 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS S 81 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS S 66 " --> pdb=" O ARG S 77 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP S 79 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS S 64 " --> pdb=" O ASP S 79 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS S 81 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL S 62 " --> pdb=" O LYS S 81 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA S 83 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR S 60 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL S 85 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL S 58 " --> pdb=" O VAL S 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 40 through 46 removed outlier: 5.111A pdb=" N ASN T 40 " --> pdb=" O ALA T 63 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 83 through 87 Processing sheet with id= 39, first strand: chain 'U' and resid 69 through 72 removed outlier: 6.658A pdb=" N ALA U 39 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE U 89 " --> pdb=" O PRO U 27 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.412A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 65 through 71 Processing sheet with id= 42, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.633A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 35 through 41 Processing sheet with id= 44, first strand: chain 'Y' and resid 33 through 39 removed outlier: 4.034A pdb=" N HIS Y 34 " --> pdb=" O GLN Y 9 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N MET Y 54 " --> pdb=" O THR Y 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 20 through 25 removed outlier: 4.113A pdb=" N ASN Z 20 " --> pdb=" O CYS Z 16 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'a' and resid 29 through 32 removed outlier: 4.399A pdb=" N GLU a 36 " --> pdb=" O ASP a 31 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 19 through 26 removed outlier: 6.048A pdb=" N HIS b 19 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE b 48 " --> pdb=" O SER b 14 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU b 34 " --> pdb=" O GLU b 51 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'd' and resid 22 through 25 removed outlier: 5.499A pdb=" N PHE d 22 " --> pdb=" O VAL d 50 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 13 through 19 removed outlier: 8.029A pdb=" N ASN e 13 " --> pdb=" O SER e 28 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'f' and resid 15 through 18 removed outlier: 5.187A pdb=" N HIS f 15 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY f 17 " --> pdb=" O HIS f 39 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS f 39 " --> pdb=" O GLY f 17 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'f' and resid 89 through 93 Processing sheet with id= 52, first strand: chain 'g' and resid 53 through 59 removed outlier: 3.730A pdb=" N ARG g 54 " --> pdb=" O HIS g 69 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'g' and resid 164 through 169 removed outlier: 6.052A pdb=" N ARG g 164 " --> pdb=" O GLY g 155 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASP g 181 " --> pdb=" O LYS g 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 141 through 145 removed outlier: 6.529A pdb=" N MET h 178 " --> pdb=" O ILE h 145 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'i' and resid 11 through 16 removed outlier: 7.112A pdb=" N LEU i 36 " --> pdb=" O ILE i 16 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 84 through 88 removed outlier: 3.712A pdb=" N ALA i 99 " --> pdb=" O ASN i 122 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN i 122 " --> pdb=" O ALA i 99 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 33 through 41 removed outlier: 6.709A pdb=" N ARG i 45 " --> pdb=" O ASP i 41 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 38 through 42 removed outlier: 3.938A pdb=" N ARG j 38 " --> pdb=" O ASN j 63 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR j 59 " --> pdb=" O TRP j 42 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS j 3 " --> pdb=" O THR j 92 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 43 through 47 removed outlier: 3.742A pdb=" N GLY j 43 " --> pdb=" O TYR j 59 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N HIS j 55 " --> pdb=" O LEU j 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 72 through 79 removed outlier: 6.048A pdb=" N THR k 72 " --> pdb=" O VAL k 91 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR k 85 " --> pdb=" O ARG k 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 23 through 29 removed outlier: 6.805A pdb=" N ALA l 23 " --> pdb=" O LEU l 63 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP l 48 " --> pdb=" O THR l 62 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 74 through 77 removed outlier: 3.712A pdb=" N CYS l 127 " --> pdb=" O VAL l 103 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL l 103 " --> pdb=" O ILE l 126 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 5 through 11 removed outlier: 4.073A pdb=" N LYS m 27 " --> pdb=" O LEU m 61 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'n' and resid 35 through 38 removed outlier: 7.604A pdb=" N GLN n 35 " --> pdb=" O VAL n 77 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP n 75 " --> pdb=" O ARG n 37 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG n 5 " --> pdb=" O GLY n 103 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'n' and resid 40 through 52 removed outlier: 6.132A pdb=" N LEU n 73 " --> pdb=" O PRO n 41 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU n 71 " --> pdb=" O PRO n 43 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'o' and resid 30 through 36 Processing sheet with id= 67, first strand: chain 'p' and resid 29 through 33 removed outlier: 5.297A pdb=" N LEU p 81 " --> pdb=" O VAL p 98 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS p 96 " --> pdb=" O ARG p 83 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 36 through 41 removed outlier: 5.170A pdb=" N LYS p 51 " --> pdb=" O ILE p 67 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 't' and resid 4 through 10 removed outlier: 4.168A pdb=" N PHE t 16 " --> pdb=" O HIS t 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY t 37 " --> pdb=" O VAL t 19 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY t 49 " --> pdb=" O ASN t 40 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'u' and resid 7 through 11 removed outlier: 7.219A pdb=" N GLU u 60 " --> pdb=" O VAL u 76 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER u 72 " --> pdb=" O CYS u 64 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'u' and resid 19 through 30 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'w' and resid 30 through 33 removed outlier: 4.452A pdb=" N LEU w 47 " --> pdb=" O VAL w 62 " (cutoff:3.500A) 1961 hydrogen bonds defined for protein. 5805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3957 hydrogen bonds 6230 hydrogen bond angles 0 basepair planarities 1572 basepair parallelities 2585 stacking parallelities Total time for adding SS restraints: 287.34 Time building geometry restraints manager: 70.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.19: 28 1.19 - 1.35: 37654 1.35 - 1.50: 77549 1.50 - 1.66: 41818 1.66 - 1.81: 270 Bond restraints: 157319 Sorted by residual: bond pdb=" C5 5MU z 66 " pdb=" C6 5MU z 66 " ideal model delta sigma weight residual 1.155 1.445 -0.290 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.433 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.595 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.598 0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 157314 not shown) Histogram of bond angle deviations from ideal: 42.08 - 63.03: 3 63.03 - 83.99: 3 83.99 - 104.94: 21573 104.94 - 125.89: 198810 125.89 - 146.85: 15049 Bond angle restraints: 235438 Sorted by residual: angle pdb=" OP1 U z 8 " pdb=" P U z 8 " pdb=" OP3 U z 8 " ideal model delta sigma weight residual 109.47 42.08 67.39 3.00e+00 1.11e-01 5.05e+02 angle pdb=" OP1 U z 67 " pdb=" P U z 67 " pdb=" OP3 U z 67 " ideal model delta sigma weight residual 109.47 43.45 66.02 3.00e+00 1.11e-01 4.84e+02 angle pdb=" O6 OMG z 17 " pdb=" C6 OMG z 17 " pdb=" N1 OMG z 17 " ideal model delta sigma weight residual 119.94 62.50 57.44 3.00e+00 1.11e-01 3.67e+02 angle pdb=" C5 OMG z 17 " pdb=" C6 OMG z 17 " pdb=" O6 OMG z 17 " ideal model delta sigma weight residual 120.11 63.67 56.44 3.00e+00 1.11e-01 3.54e+02 angle pdb=" OP1 G z 9 " pdb=" P G z 9 " pdb=" OP3 G z 9 " ideal model delta sigma weight residual 109.47 79.63 29.84 3.00e+00 1.11e-01 9.89e+01 ... (remaining 235433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 88672 35.90 - 71.80: 11115 71.80 - 107.69: 820 107.69 - 143.59: 20 143.59 - 179.49: 43 Dihedral angle restraints: 100670 sinusoidal: 84340 harmonic: 16330 Sorted by residual: dihedral pdb=" C4* PSU 2 516 " pdb=" C3* PSU 2 516 " pdb=" C2* PSU 2 516 " pdb=" C1* PSU 2 516 " ideal model delta sinusoidal sigma weight residual -35.00 37.32 -72.32 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C5* PSU 2 516 " pdb=" C4* PSU 2 516 " pdb=" C3* PSU 2 516 " pdb=" O3* PSU 2 516 " ideal model delta sinusoidal sigma weight residual 147.00 76.04 70.96 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' C 12146 " pdb=" C3' C 12146 " pdb=" C2' C 12146 " pdb=" C1' C 12146 " ideal model delta sinusoidal sigma weight residual -35.00 33.55 -68.55 1 8.00e+00 1.56e-02 9.51e+01 ... (remaining 100667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.459: 29988 0.459 - 0.917: 4 0.917 - 1.376: 1 1.376 - 1.835: 0 1.835 - 2.293: 1 Chirality restraints: 29994 Sorted by residual: chirality pdb=" P U z 20 " pdb=" OP1 U z 20 " pdb=" OP2 U z 20 " pdb=" O5' U z 20 " both_signs ideal model delta sigma weight residual True 2.41 -0.12 2.29 2.00e-01 2.50e+01 1.31e+02 chirality pdb=" P G z 9 " pdb=" OP1 G z 9 " pdb=" OP2 G z 9 " pdb=" O5' G z 9 " both_signs ideal model delta sigma weight residual True 2.41 -1.28 1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" C1* PSU 12580 " pdb=" O4* PSU 12580 " pdb=" C2* PSU 12580 " pdb=" C5 PSU 12580 " both_signs ideal model delta sigma weight residual False 2.55 1.77 0.78 2.00e-01 2.50e+01 1.53e+01 ... (remaining 29991 not shown) Planarity restraints: 12546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.102 2.00e-02 2.50e+03 6.55e-01 9.65e+03 pdb=" C4' 2MG 21516 " -0.484 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.745 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.584 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.717 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.165 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -1.019 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.169 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 1.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU z 66 " 0.065 2.00e-02 2.50e+03 6.33e-01 9.02e+03 pdb=" C4' 5MU z 66 " 0.482 2.00e-02 2.50e+03 pdb=" O4' 5MU z 66 " 0.803 2.00e-02 2.50e+03 pdb=" C3' 5MU z 66 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 5MU z 66 " -0.637 2.00e-02 2.50e+03 pdb=" C2' 5MU z 66 " -0.212 2.00e-02 2.50e+03 pdb=" O2' 5MU z 66 " 0.931 2.00e-02 2.50e+03 pdb=" C1' 5MU z 66 " 0.171 2.00e-02 2.50e+03 pdb=" N1 5MU z 66 " -1.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12498 " -0.069 2.00e-02 2.50e+03 6.04e-01 8.20e+03 pdb=" C4' OMC 12498 " -0.430 2.00e-02 2.50e+03 pdb=" O4' OMC 12498 " -0.598 2.00e-02 2.50e+03 pdb=" C3' OMC 12498 " 0.607 2.00e-02 2.50e+03 pdb=" O3' OMC 12498 " 0.661 2.00e-02 2.50e+03 pdb=" C2' OMC 12498 " 0.153 2.00e-02 2.50e+03 pdb=" O2' OMC 12498 " -1.007 2.00e-02 2.50e+03 pdb=" C1' OMC 12498 " -0.231 2.00e-02 2.50e+03 pdb=" N1 OMC 12498 " 0.915 2.00e-02 2.50e+03 ... (remaining 12543 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 351 2.14 - 2.83: 43217 2.83 - 3.52: 207169 3.52 - 4.21: 476978 4.21 - 4.90: 630801 Nonbonded interactions: 1358516 Sorted by model distance: nonbonded pdb=" O3' A z 88 " pdb=" C SER B 27 " model vdw 1.449 3.270 nonbonded pdb=" O6 OMG z 17 " pdb=" C2 OMG z 17 " model vdw 1.674 2.608 nonbonded pdb=" OP2 C 12499 " pdb="MG MG 13082 " model vdw 1.719 2.170 nonbonded pdb=" O6 OMG z 17 " pdb=" C4 OMG z 17 " model vdw 1.722 2.608 nonbonded pdb=" OP2 G 11828 " pdb="MG MG 13092 " model vdw 1.722 2.170 ... (remaining 1358511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.100 Extract box with map and model: 18.260 Check model and map are aligned: 1.570 Set scattering table: 0.990 Process input model: 608.060 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 637.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.011 0.290 157319 Z= 0.680 Angle : 1.024 67.392 235438 Z= 0.538 Chirality : 0.061 2.293 29994 Planarity : 0.021 0.655 12546 Dihedral : 22.866 179.491 90138 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 0.21 % Allowed : 2.86 % Favored : 96.93 % Cbeta Deviations : 0.00 % 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: -3.86 (0.09), residues: 5634 helix: -3.59 (0.06), residues: 1933 sheet: -1.85 (0.14), residues: 1155 loop : -1.85 (0.11), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP E 78 HIS 0.019 0.003 HIS C 230 PHE 0.078 0.003 PHE M 80 TYR 0.039 0.003 TYR b 49 ARG 0.032 0.002 ARG c 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1813 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1803 time to evaluate : 6.365 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.7566 (m-30) cc_final: 0.7299 (m-30) REVERT: C 121 ASP cc_start: 0.8469 (p0) cc_final: 0.8108 (p0) REVERT: C 180 GLU cc_start: 0.7076 (tt0) cc_final: 0.6872 (tt0) REVERT: E 1 MET cc_start: 0.7694 (tpt) cc_final: 0.7453 (tpp) REVERT: E 149 ILE cc_start: 0.8966 (pt) cc_final: 0.7798 (pt) REVERT: F 35 THR cc_start: 0.9006 (m) cc_final: 0.8674 (p) REVERT: F 77 PHE cc_start: 0.6849 (m-10) cc_final: 0.5919 (m-10) REVERT: G 104 ASN cc_start: 0.8049 (m110) cc_final: 0.7289 (m-40) REVERT: I 98 GLU cc_start: 0.8201 (mp0) cc_final: 0.7865 (mp0) REVERT: J 59 LYS cc_start: 0.8819 (mttt) cc_final: 0.8612 (mttp) REVERT: P 32 TYR cc_start: 0.8251 (t80) cc_final: 0.7820 (t80) REVERT: P 91 ASP cc_start: 0.7150 (p0) cc_final: 0.6822 (p0) REVERT: R 15 GLN cc_start: 0.8153 (tt0) cc_final: 0.7943 (tt0) REVERT: S 27 SER cc_start: 0.8926 (m) cc_final: 0.8599 (p) REVERT: S 70 HIS cc_start: 0.7540 (t70) cc_final: 0.7331 (t70) REVERT: Z 21 VAL cc_start: 0.9440 (t) cc_final: 0.9238 (p) REVERT: Z 63 ARG cc_start: 0.7425 (mtp85) cc_final: 0.6988 (mtp85) REVERT: Z 65 ASN cc_start: 0.8107 (m-40) cc_final: 0.7702 (m110) REVERT: a 7 LYS cc_start: 0.9297 (tttt) cc_final: 0.9039 (tttt) REVERT: b 27 LYS cc_start: 0.8314 (mttt) cc_final: 0.8037 (mttm) REVERT: d 32 ILE cc_start: 0.9004 (mt) cc_final: 0.8802 (mt) REVERT: f 170 HIS cc_start: 0.8395 (p-80) cc_final: 0.7867 (p-80) REVERT: h 4 TYR cc_start: 0.8319 (t80) cc_final: 0.7990 (t80) REVERT: k 148 ASN cc_start: 0.8968 (m-40) cc_final: 0.8686 (m-40) REVERT: l 61 LEU cc_start: 0.9087 (mt) cc_final: 0.8748 (mt) REVERT: l 113 ASP cc_start: 0.8333 (p0) cc_final: 0.8115 (p0) REVERT: m 50 GLN cc_start: 0.8215 (mt0) cc_final: 0.7930 (mt0) REVERT: n 25 ILE cc_start: 0.9248 (mm) cc_final: 0.8986 (tp) REVERT: n 98 VAL cc_start: 0.8901 (m) cc_final: 0.8633 (t) REVERT: o 18 ASP cc_start: 0.8330 (p0) cc_final: 0.8023 (p0) REVERT: o 84 VAL cc_start: 0.9337 (t) cc_final: 0.8693 (m) REVERT: o 111 THR cc_start: 0.8693 (m) cc_final: 0.8291 (m) REVERT: q 54 ASP cc_start: 0.8156 (m-30) cc_final: 0.5643 (m-30) REVERT: r 33 ASP cc_start: 0.6804 (t0) cc_final: 0.6225 (t70) REVERT: r 35 ASN cc_start: 0.8248 (m-40) cc_final: 0.7959 (p0) REVERT: r 92 GLU cc_start: 0.7974 (mp0) cc_final: 0.7719 (mp0) REVERT: s 2 SER cc_start: 0.8796 (m) cc_final: 0.8594 (p) REVERT: t 12 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8509 (ttmm) REVERT: t 76 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8584 (ptmt) REVERT: u 7 THR cc_start: 0.8442 (t) cc_final: 0.8003 (t) REVERT: u 41 THR cc_start: 0.8620 (m) cc_final: 0.8244 (m) REVERT: u 60 GLU cc_start: 0.7491 (tt0) cc_final: 0.6938 (tt0) REVERT: v 21 ILE cc_start: 0.9134 (mt) cc_final: 0.8926 (mt) REVERT: v 25 ASP cc_start: 0.7659 (t0) cc_final: 0.7348 (t0) REVERT: v 26 ILE cc_start: 0.8890 (mt) cc_final: 0.8580 (mm) REVERT: w 5 LEU cc_start: 0.8818 (mt) cc_final: 0.8593 (mt) REVERT: w 63 THR cc_start: 0.8631 (m) cc_final: 0.8147 (p) REVERT: x 82 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8400 (mm-40) REVERT: y 31 GLU cc_start: 0.7899 (tp30) cc_final: 0.7608 (tp30) outliers start: 10 outliers final: 4 residues processed: 1809 average time/residue: 1.4191 time to fit residues: 4393.8627 Evaluate side-chains 1275 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1271 time to evaluate : 6.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain f residue 129 LEU Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain B residue 16 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 855 optimal weight: 5.9990 chunk 767 optimal weight: 8.9990 chunk 426 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 517 optimal weight: 5.9990 chunk 410 optimal weight: 10.0000 chunk 793 optimal weight: 9.9990 chunk 307 optimal weight: 20.0000 chunk 482 optimal weight: 8.9990 chunk 590 optimal weight: 5.9990 chunk 919 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN C 70 ASN C 163 GLN D 49 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN G 20 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 HIS I 86 GLN J 3 GLN J 5 GLN J 9 ASN J 89 ASN M 9 GLN O 10 GLN O 56 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN S 48 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 16 ASN g 19 ASN g 190 HIS h 54 GLN i 61 GLN i 70 ASN j 3 HIS m 31 ASN m 32 GLN m 81 HIS n 56 HIS o 38 GLN o 119 ASN p 6 GLN ** p 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 59 HIS u 9 GLN v 31 ASN ** v 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 3 ASN x 20 HIS x 21 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 157319 Z= 0.256 Angle : 0.718 59.269 235438 Z= 0.368 Chirality : 0.037 1.203 29994 Planarity : 0.007 0.130 12546 Dihedral : 23.848 179.964 78858 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.07 % Rotamer: Outliers : 2.88 % Allowed : 13.73 % Favored : 83.39 % Cbeta Deviations : 0.00 % 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: -1.52 (0.10), residues: 5634 helix: -0.47 (0.11), residues: 1937 sheet: -1.16 (0.15), residues: 1088 loop : -1.25 (0.11), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 11 HIS 0.011 0.001 HIS g 6 PHE 0.032 0.002 PHE F 100 TYR 0.029 0.002 TYR m 90 ARG 0.016 0.001 ARG X 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1667 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1532 time to evaluate : 6.472 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: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.7650 (tptt) cc_final: 0.7388 (tptt) REVERT: C 121 ASP cc_start: 0.8432 (p0) cc_final: 0.8170 (p0) REVERT: F 35 THR cc_start: 0.9160 (m) cc_final: 0.8915 (p) REVERT: F 52 ASN cc_start: 0.8081 (t0) cc_final: 0.7874 (t0) REVERT: F 77 PHE cc_start: 0.6935 (m-10) cc_final: 0.5493 (m-10) REVERT: F 121 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.8018 (p) REVERT: G 95 ARG cc_start: 0.8073 (ptm-80) cc_final: 0.7804 (ptm-80) REVERT: I 81 ILE cc_start: 0.8541 (tp) cc_final: 0.8080 (tp) REVERT: I 138 GLN cc_start: 0.8088 (mp10) cc_final: 0.7419 (mp10) REVERT: J 89 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7187 (m-40) REVERT: L 136 MET cc_start: 0.5370 (ttp) cc_final: 0.4998 (tmm) REVERT: O 106 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8613 (mmtp) REVERT: P 32 TYR cc_start: 0.8499 (t80) cc_final: 0.8245 (t80) REVERT: P 44 GLN cc_start: 0.8317 (mt0) cc_final: 0.8071 (mt0) REVERT: Q 101 ILE cc_start: 0.8517 (mt) cc_final: 0.8264 (mt) REVERT: S 24 MET cc_start: 0.7268 (tmm) cc_final: 0.7063 (ppp) REVERT: S 27 SER cc_start: 0.8914 (m) cc_final: 0.8631 (p) REVERT: b 8 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8839 (mtmt) REVERT: j 25 TYR cc_start: 0.8885 (m-10) cc_final: 0.8673 (m-10) REVERT: j 42 TRP cc_start: 0.7969 (m-10) cc_final: 0.7769 (m-10) REVERT: j 88 MET cc_start: 0.7738 (tmm) cc_final: 0.7328 (tmm) REVERT: j 102 MET cc_start: 0.6893 (ptm) cc_final: 0.6631 (ptm) REVERT: l 90 ASP cc_start: 0.7192 (p0) cc_final: 0.6559 (p0) REVERT: l 113 ASP cc_start: 0.8173 (p0) cc_final: 0.7804 (p0) REVERT: m 6 TYR cc_start: 0.7408 (m-10) cc_final: 0.7205 (m-10) REVERT: o 18 ASP cc_start: 0.8415 (p0) cc_final: 0.7910 (p0) REVERT: o 32 VAL cc_start: 0.8961 (t) cc_final: 0.8642 (p) REVERT: q 50 GLU cc_start: 0.6245 (tm-30) cc_final: 0.5641 (tm-30) REVERT: q 54 ASP cc_start: 0.7325 (m-30) cc_final: 0.6330 (m-30) REVERT: q 69 LEU cc_start: 0.9176 (mt) cc_final: 0.8917 (mt) REVERT: q 78 LYS cc_start: 0.9225 (ttmt) cc_final: 0.8820 (tppt) REVERT: q 104 THR cc_start: 0.8651 (m) cc_final: 0.8330 (p) REVERT: r 33 ASP cc_start: 0.6824 (t0) cc_final: 0.6467 (t70) REVERT: t 12 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8599 (ttmm) REVERT: u 28 PHE cc_start: 0.7750 (t80) cc_final: 0.7176 (t80) REVERT: u 52 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: v 13 PHE cc_start: 0.7605 (m-80) cc_final: 0.7381 (m-80) REVERT: v 25 ASP cc_start: 0.8069 (t0) cc_final: 0.7481 (t0) REVERT: w 61 PHE cc_start: 0.8136 (t80) cc_final: 0.7924 (t80) REVERT: x 57 ILE cc_start: 0.9221 (mt) cc_final: 0.8988 (mm) outliers start: 135 outliers final: 74 residues processed: 1579 average time/residue: 1.2581 time to fit residues: 3433.2158 Evaluate side-chains 1421 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1344 time to evaluate : 6.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain I residue 55 ILE Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 90 ASN Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 68 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 38 VAL Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 32 CYS Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 121 HIS Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain k residue 66 LEU Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 34 ILE Chi-restraints excluded: chain o residue 36 ASP Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 62 ASN Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain u residue 52 GLU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 19 VAL Chi-restraints excluded: chain x residue 3 ASN Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 511 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 chunk 765 optimal weight: 20.0000 chunk 626 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 921 optimal weight: 9.9990 chunk 995 optimal weight: 9.9990 chunk 820 optimal weight: 5.9990 chunk 913 optimal weight: 10.0000 chunk 314 optimal weight: 20.0000 chunk 739 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN C 163 GLN C 239 ASN D 130 GLN D 136 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN H 43 ASN I 86 GLN J 3 GLN J 5 GLN N 61 GLN O 10 GLN O 15 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 82 HIS R 40 ASN S 70 HIS Z 65 ASN ** f 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 HIS g 190 HIS h 140 ASN ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 130 ASN l 4 GLN m 75 GLN o 119 ASN ** p 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 157319 Z= 0.284 Angle : 0.683 59.573 235438 Z= 0.352 Chirality : 0.036 1.181 29994 Planarity : 0.006 0.132 12546 Dihedral : 23.699 179.243 78854 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.37 % Allowed : 16.38 % Favored : 80.25 % Cbeta Deviations : 0.00 % 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: -0.58 (0.11), residues: 5634 helix: 0.70 (0.12), residues: 1943 sheet: -0.78 (0.15), residues: 1069 loop : -0.97 (0.11), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP j 42 HIS 0.009 0.001 HIS N 100 PHE 0.022 0.002 PHE F 100 TYR 0.024 0.002 TYR i 128 ARG 0.010 0.001 ARG j 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1576 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1418 time to evaluate : 6.467 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: C 121 ASP cc_start: 0.8457 (p0) cc_final: 0.8179 (p0) REVERT: F 77 PHE cc_start: 0.7012 (m-10) cc_final: 0.5292 (m-10) REVERT: F 121 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8136 (p) REVERT: F 155 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8829 (p) REVERT: G 95 ARG cc_start: 0.8017 (ptm-80) cc_final: 0.7357 (ptm-80) REVERT: L 136 MET cc_start: 0.5820 (ttp) cc_final: 0.5478 (tmm) REVERT: M 14 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.8139 (t) REVERT: M 74 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6899 (tm-30) REVERT: Q 85 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8490 (mtpt) REVERT: R 86 MET cc_start: 0.7425 (tpt) cc_final: 0.7141 (tpt) REVERT: S 27 SER cc_start: 0.8857 (m) cc_final: 0.8459 (p) REVERT: S 73 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7784 (tpp80) REVERT: T 37 GLU cc_start: 0.7530 (pp20) cc_final: 0.7072 (pp20) REVERT: W 43 GLU cc_start: 0.7264 (mp0) cc_final: 0.6863 (mp0) REVERT: X 25 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7745 (tp-100) REVERT: b 8 LYS cc_start: 0.9119 (mtmt) cc_final: 0.8856 (mtmt) REVERT: b 35 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6631 (mm-30) REVERT: j 2 ARG cc_start: 0.7260 (mtp85) cc_final: 0.7041 (mtt-85) REVERT: j 25 TYR cc_start: 0.8927 (m-10) cc_final: 0.8697 (m-10) REVERT: j 88 MET cc_start: 0.7670 (tmm) cc_final: 0.7371 (tmm) REVERT: l 113 ASP cc_start: 0.8369 (p0) cc_final: 0.7904 (p0) REVERT: m 91 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7275 (p0) REVERT: o 32 VAL cc_start: 0.9121 (t) cc_final: 0.8717 (p) REVERT: o 34 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8750 (mm) REVERT: o 79 ILE cc_start: 0.8781 (mm) cc_final: 0.8441 (tp) REVERT: o 126 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8628 (mtpp) REVERT: q 50 GLU cc_start: 0.6467 (tm-30) cc_final: 0.5785 (tm-30) REVERT: q 54 ASP cc_start: 0.7686 (m-30) cc_final: 0.6939 (m-30) REVERT: q 78 LYS cc_start: 0.9227 (ttmt) cc_final: 0.8929 (tppt) REVERT: q 81 MET cc_start: 0.8703 (mmp) cc_final: 0.7919 (mmp) REVERT: t 12 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8671 (ttmm) REVERT: v 25 ASP cc_start: 0.8028 (t0) cc_final: 0.7673 (t0) REVERT: y 31 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7457 (tm-30) outliers start: 158 outliers final: 104 residues processed: 1469 average time/residue: 1.2588 time to fit residues: 3221.2497 Evaluate side-chains 1421 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1312 time to evaluate : 6.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain I residue 55 ILE Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 68 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 109 ASP Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 49 ASN Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 32 CYS Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 121 HIS Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 54 LEU Chi-restraints excluded: chain j residue 55 HIS Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 91 ASP Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 25 ILE Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 92 LEU Chi-restraints excluded: chain o residue 34 ILE Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 83 LEU Chi-restraints excluded: chain r residue 62 ASN Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 43 ASN Chi-restraints excluded: chain w residue 51 VAL Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain x residue 3 ASN Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 36 GLU Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 910 optimal weight: 20.0000 chunk 692 optimal weight: 3.9990 chunk 478 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 439 optimal weight: 20.0000 chunk 618 optimal weight: 0.0470 chunk 924 optimal weight: 3.9990 chunk 979 optimal weight: 6.9990 chunk 483 optimal weight: 9.9990 chunk 876 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 226 ASN D 130 GLN D 150 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN I 86 GLN J 3 GLN J 5 GLN O 10 GLN O 15 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 ASN f 120 GLN g 19 ASN ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN k 130 ASN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 ASN q 14 HIS ** t 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 75 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.180 157319 Z= 0.206 Angle : 0.655 59.360 235438 Z= 0.339 Chirality : 0.034 1.183 29994 Planarity : 0.006 0.125 12546 Dihedral : 23.655 179.564 78854 Min Nonbonded Distance : 1.236 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.73 % Allowed : 17.89 % Favored : 78.37 % 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: -0.25 (0.11), residues: 5634 helix: 1.00 (0.12), residues: 1966 sheet: -0.54 (0.16), residues: 1055 loop : -0.85 (0.12), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 11 HIS 0.007 0.001 HIS N 100 PHE 0.019 0.001 PHE v 13 TYR 0.021 0.002 TYR i 128 ARG 0.010 0.001 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1585 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1410 time to evaluate : 6.384 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: C 5 LYS cc_start: 0.7782 (tptt) cc_final: 0.7540 (tptt) REVERT: C 121 ASP cc_start: 0.8465 (p0) cc_final: 0.8199 (p0) REVERT: F 77 PHE cc_start: 0.7022 (m-10) cc_final: 0.5584 (m-10) REVERT: F 121 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.8002 (p) REVERT: F 155 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8813 (p) REVERT: L 136 MET cc_start: 0.5737 (ttp) cc_final: 0.5395 (tmm) REVERT: M 14 SER cc_start: 0.8419 (OUTLIER) cc_final: 0.8207 (t) REVERT: M 72 ASP cc_start: 0.6910 (t0) cc_final: 0.6686 (t0) REVERT: M 74 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6911 (pp20) REVERT: R 86 MET cc_start: 0.7412 (tpt) cc_final: 0.7153 (tpt) REVERT: S 25 GLU cc_start: 0.7609 (pp20) cc_final: 0.7049 (pp20) REVERT: S 27 SER cc_start: 0.8806 (m) cc_final: 0.8503 (p) REVERT: S 73 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7923 (tpp80) REVERT: T 37 GLU cc_start: 0.7466 (pp20) cc_final: 0.7151 (pp20) REVERT: i 142 ASP cc_start: 0.7429 (t0) cc_final: 0.7193 (t0) REVERT: j 25 TYR cc_start: 0.8875 (m-10) cc_final: 0.8671 (m-10) REVERT: j 88 MET cc_start: 0.7996 (tmm) cc_final: 0.7746 (tmm) REVERT: l 113 ASP cc_start: 0.8372 (p0) cc_final: 0.7840 (p0) REVERT: o 32 VAL cc_start: 0.9038 (t) cc_final: 0.8684 (p) REVERT: o 34 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8580 (mm) REVERT: o 126 LYS cc_start: 0.8991 (ttmm) cc_final: 0.8692 (mtpp) REVERT: q 8 ASN cc_start: 0.7438 (t0) cc_final: 0.7148 (t0) REVERT: q 50 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6137 (tm-30) REVERT: q 54 ASP cc_start: 0.7747 (m-30) cc_final: 0.6941 (m-30) REVERT: q 78 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8995 (tppt) REVERT: t 12 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8618 (ttmm) REVERT: y 31 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7396 (tm-30) outliers start: 175 outliers final: 119 residues processed: 1474 average time/residue: 1.2239 time to fit residues: 3140.7721 Evaluate side-chains 1443 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1320 time to evaluate : 6.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 106 GLU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain O residue 68 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 109 ASP Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 27 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain f residue 120 GLN Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 32 CYS Chi-restraints excluded: chain h residue 124 MET Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 121 HIS Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 13 ASP Chi-restraints excluded: chain j residue 54 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain n residue 10 LEU Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 25 ILE Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 34 ILE Chi-restraints excluded: chain o residue 36 ASP Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 73 ASN Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 35 ASN Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 20 GLU Chi-restraints excluded: chain w residue 51 VAL Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain x residue 3 ASN Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 59 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 815 optimal weight: 7.9990 chunk 555 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 729 optimal weight: 20.0000 chunk 404 optimal weight: 20.0000 chunk 835 optimal weight: 20.0000 chunk 676 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 499 optimal weight: 8.9990 chunk 878 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 115 GLN G 22 GLN I 86 GLN I 138 GLN J 3 GLN J 5 GLN J 89 ASN P 72 ASN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 HIS R 40 ASN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 ASN e 13 ASN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 19 ASN ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** t 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 3 ASN y 56 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 157319 Z= 0.311 Angle : 0.686 59.505 235438 Z= 0.353 Chirality : 0.037 1.196 29994 Planarity : 0.006 0.131 12546 Dihedral : 23.590 179.564 78854 Min Nonbonded Distance : 1.026 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.31 % Allowed : 18.79 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 5634 helix: 1.14 (0.12), residues: 1950 sheet: -0.44 (0.16), residues: 1072 loop : -0.75 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 11 HIS 0.008 0.001 HIS N 100 PHE 0.024 0.002 PHE H 47 TYR 0.023 0.002 TYR i 128 ARG 0.011 0.001 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1366 time to evaluate : 8.743 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: C 5 LYS cc_start: 0.7799 (tptt) cc_final: 0.7515 (tptt) REVERT: C 121 ASP cc_start: 0.8498 (p0) cc_final: 0.8222 (p0) REVERT: F 77 PHE cc_start: 0.7144 (m-80) cc_final: 0.5804 (m-10) REVERT: F 121 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8128 (p) REVERT: F 155 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8857 (p) REVERT: J 89 ASN cc_start: 0.7737 (m110) cc_final: 0.7447 (t0) REVERT: L 1 MET cc_start: 0.7887 (tpp) cc_final: 0.7490 (tpt) REVERT: L 136 MET cc_start: 0.5809 (ttp) cc_final: 0.5466 (tmm) REVERT: M 14 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.8201 (t) REVERT: M 72 ASP cc_start: 0.7045 (t0) cc_final: 0.6842 (t0) REVERT: Q 85 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8737 (mtpp) REVERT: R 86 MET cc_start: 0.7441 (tpt) cc_final: 0.7164 (tpt) REVERT: S 27 SER cc_start: 0.8826 (m) cc_final: 0.8459 (p) REVERT: S 73 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7874 (tpp80) REVERT: T 62 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7593 (mt-10) REVERT: W 43 GLU cc_start: 0.7474 (mp0) cc_final: 0.7020 (mp0) REVERT: Z 11 GLU cc_start: 0.8010 (tp30) cc_final: 0.7296 (tp30) REVERT: c 1 MET cc_start: 0.7897 (mmm) cc_final: 0.7621 (mmm) REVERT: l 113 ASP cc_start: 0.8388 (p0) cc_final: 0.7878 (p0) REVERT: m 63 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8672 (mp) REVERT: o 32 VAL cc_start: 0.9098 (t) cc_final: 0.8758 (p) REVERT: o 34 ILE cc_start: 0.8964 (mm) cc_final: 0.8689 (mm) REVERT: o 126 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8718 (mtpp) REVERT: p 62 GLU cc_start: 0.7972 (tp30) cc_final: 0.7743 (tp30) REVERT: q 50 GLU cc_start: 0.6649 (tm-30) cc_final: 0.6251 (tm-30) REVERT: q 54 ASP cc_start: 0.7667 (m-30) cc_final: 0.6795 (m-30) REVERT: q 78 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8978 (tppt) REVERT: q 81 MET cc_start: 0.8682 (mmp) cc_final: 0.8144 (mmm) REVERT: v 25 ASP cc_start: 0.8077 (t0) cc_final: 0.7415 (t0) REVERT: y 31 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7446 (tm-30) outliers start: 202 outliers final: 145 residues processed: 1444 average time/residue: 1.3138 time to fit residues: 3322.9593 Evaluate side-chains 1452 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1302 time to evaluate : 6.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 61 ARG Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 55 ILE Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 68 GLU Chi-restraints excluded: chain O residue 85 SER Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 85 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 109 ASP Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 27 LEU Chi-restraints excluded: chain Y residue 49 ASN Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain b residue 10 LYS Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 32 CYS Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 121 HIS Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 13 ASP Chi-restraints excluded: chain j residue 54 LEU Chi-restraints excluded: chain j residue 55 HIS Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 111 VAL Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 25 ILE Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain o residue 17 SER Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 36 ASP Chi-restraints excluded: chain o residue 42 LEU Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain o residue 100 LEU Chi-restraints excluded: chain o residue 110 ILE Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain t residue 76 LYS Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 43 LYS Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 55 ILE Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 5 LEU Chi-restraints excluded: chain w residue 12 ASP Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain x residue 3 ASN Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 SER Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 329 optimal weight: 20.0000 chunk 881 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 574 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 980 optimal weight: 4.9990 chunk 813 optimal weight: 9.9990 chunk 453 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 514 optimal weight: 0.0070 overall best weight: 5.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 97 ASN E 115 GLN H 11 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 5 GLN M 9 GLN O 15 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN R 40 ASN Z 65 ASN f 120 GLN f 227 GLN g 19 ASN ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 54 GLN i 12 GLN k 130 ASN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN n 56 HIS q 8 ASN ** t 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 157319 Z= 0.252 Angle : 0.669 59.368 235438 Z= 0.345 Chirality : 0.035 1.190 29994 Planarity : 0.006 0.127 12546 Dihedral : 23.594 179.082 78854 Min Nonbonded Distance : 1.095 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.67 % Allowed : 20.77 % Favored : 75.56 % 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: 0.01 (0.11), residues: 5634 helix: 1.18 (0.12), residues: 1953 sheet: -0.36 (0.16), residues: 1059 loop : -0.67 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 201 HIS 0.007 0.001 HIS N 100 PHE 0.022 0.001 PHE g 23 TYR 0.024 0.002 TYR i 128 ARG 0.011 0.000 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1364 time to evaluate : 6.382 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: C 5 LYS cc_start: 0.7853 (tptt) cc_final: 0.7544 (tptt) REVERT: C 121 ASP cc_start: 0.8486 (p0) cc_final: 0.8225 (p0) REVERT: F 77 PHE cc_start: 0.7020 (m-80) cc_final: 0.5550 (m-10) REVERT: F 121 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8166 (p) REVERT: F 155 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8865 (p) REVERT: G 95 ARG cc_start: 0.7869 (ptm-80) cc_final: 0.7463 (ptm-80) REVERT: H 12 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8228 (pp) REVERT: J 89 ASN cc_start: 0.7692 (m110) cc_final: 0.7489 (t0) REVERT: L 1 MET cc_start: 0.7839 (tpp) cc_final: 0.7374 (tpt) REVERT: L 22 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7241 (tp40) REVERT: L 47 GLU cc_start: 0.7057 (pp20) cc_final: 0.6674 (pp20) REVERT: L 136 MET cc_start: 0.5891 (ttp) cc_final: 0.5656 (tmm) REVERT: Q 1 MET cc_start: 0.7472 (tmm) cc_final: 0.6864 (ttt) REVERT: Q 43 ASN cc_start: 0.7522 (t0) cc_final: 0.6631 (t0) REVERT: R 86 MET cc_start: 0.7426 (tpt) cc_final: 0.7122 (tpt) REVERT: S 27 SER cc_start: 0.8843 (m) cc_final: 0.8448 (p) REVERT: T 62 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7712 (mt-10) REVERT: c 25 LYS cc_start: 0.8611 (tmmt) cc_final: 0.8222 (tmmt) REVERT: g 42 TYR cc_start: 0.8487 (t80) cc_final: 0.8243 (t80) REVERT: i 65 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7383 (mm-30) REVERT: j 1 MET cc_start: 0.6420 (tmm) cc_final: 0.6194 (tmm) REVERT: l 113 ASP cc_start: 0.8376 (p0) cc_final: 0.7915 (p0) REVERT: n 99 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8270 (mm-40) REVERT: o 32 VAL cc_start: 0.9087 (t) cc_final: 0.8734 (p) REVERT: o 34 ILE cc_start: 0.8946 (mm) cc_final: 0.8682 (mm) REVERT: o 85 MET cc_start: 0.8305 (mmm) cc_final: 0.8050 (mmm) REVERT: o 126 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8750 (mtpp) REVERT: p 62 GLU cc_start: 0.7990 (tp30) cc_final: 0.7764 (tp30) REVERT: q 78 LYS cc_start: 0.9211 (ttmt) cc_final: 0.8986 (tppt) REVERT: q 81 MET cc_start: 0.8668 (mmp) cc_final: 0.8147 (mmm) REVERT: v 25 ASP cc_start: 0.8141 (t0) cc_final: 0.7446 (t0) REVERT: y 8 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7958 (mm-30) REVERT: y 31 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7403 (tm-30) REVERT: y 49 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8579 (tppt) outliers start: 172 outliers final: 134 residues processed: 1434 average time/residue: 1.2459 time to fit residues: 3115.2344 Evaluate side-chains 1439 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1300 time to evaluate : 6.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 68 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 109 ASP Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 27 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain f residue 120 GLN Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 121 HIS Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 13 ASP Chi-restraints excluded: chain j residue 54 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain k residue 45 SER Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 111 VAL Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 25 ILE Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 36 ASP Chi-restraints excluded: chain o residue 42 LEU Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 57 LEU Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain t residue 76 LYS Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 29 LEU Chi-restraints excluded: chain v residue 59 ILE Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 5 LEU Chi-restraints excluded: chain w residue 12 ASP Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 63 THR Chi-restraints excluded: chain x residue 3 ASN Chi-restraints excluded: chain x residue 36 TYR Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 49 LYS Chi-restraints excluded: chain y residue 51 SER Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 944 optimal weight: 3.9990 chunk 110 optimal weight: 30.0000 chunk 558 optimal weight: 0.9990 chunk 715 optimal weight: 20.0000 chunk 554 optimal weight: 8.9990 chunk 825 optimal weight: 8.9990 chunk 547 optimal weight: 10.0000 chunk 976 optimal weight: 9.9990 chunk 611 optimal weight: 6.9990 chunk 595 optimal weight: 7.9990 chunk 450 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN D 164 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 115 GLN H 11 ASN H 33 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN J 3 GLN L 88 ASN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN Z 65 ASN f 120 GLN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 19 ASN ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 130 ASN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 15 GLN ** t 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 157319 Z= 0.261 Angle : 0.674 59.323 235438 Z= 0.346 Chirality : 0.035 1.191 29994 Planarity : 0.006 0.128 12546 Dihedral : 23.572 179.202 78854 Min Nonbonded Distance : 1.097 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.71 % Allowed : 21.73 % Favored : 74.56 % 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: 0.04 (0.11), residues: 5634 helix: 1.19 (0.12), residues: 1950 sheet: -0.34 (0.16), residues: 1064 loop : -0.64 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 11 HIS 0.007 0.001 HIS N 100 PHE 0.036 0.002 PHE f 126 TYR 0.029 0.002 TYR s 78 ARG 0.012 0.001 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1518 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1344 time to evaluate : 5.831 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: C 5 LYS cc_start: 0.7926 (tptt) cc_final: 0.7692 (tptt) REVERT: C 121 ASP cc_start: 0.8485 (p0) cc_final: 0.8228 (p0) REVERT: F 77 PHE cc_start: 0.6985 (m-80) cc_final: 0.5559 (m-10) REVERT: F 121 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8181 (p) REVERT: F 155 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8847 (p) REVERT: G 95 ARG cc_start: 0.7916 (ptm-80) cc_final: 0.7504 (ptm-80) REVERT: H 12 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8320 (pp) REVERT: L 1 MET cc_start: 0.7852 (tpp) cc_final: 0.7154 (tpt) REVERT: L 22 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7242 (tp40) REVERT: Q 1 MET cc_start: 0.7522 (tmm) cc_final: 0.6919 (ttt) REVERT: S 27 SER cc_start: 0.8820 (m) cc_final: 0.8408 (p) REVERT: T 62 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7708 (mm-30) REVERT: V 44 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8206 (ttmm) REVERT: Y 11 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7228 (mtp85) REVERT: Z 65 ASN cc_start: 0.7914 (m-40) cc_final: 0.7707 (m110) REVERT: b 8 LYS cc_start: 0.9102 (ptmt) cc_final: 0.8505 (ptmt) REVERT: c 25 LYS cc_start: 0.8626 (tmmt) cc_final: 0.8288 (tmmt) REVERT: f 227 GLN cc_start: 0.6991 (pt0) cc_final: 0.6648 (pt0) REVERT: g 42 TYR cc_start: 0.8519 (t80) cc_final: 0.8267 (t80) REVERT: i 65 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7438 (mm-30) REVERT: l 113 ASP cc_start: 0.8377 (p0) cc_final: 0.7956 (p0) REVERT: n 99 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8311 (mm-40) REVERT: o 32 VAL cc_start: 0.9082 (t) cc_final: 0.8748 (p) REVERT: o 34 ILE cc_start: 0.8977 (mm) cc_final: 0.8714 (mm) REVERT: o 108 THR cc_start: 0.9129 (m) cc_final: 0.8839 (p) REVERT: o 126 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8828 (mtpp) REVERT: p 62 GLU cc_start: 0.7969 (tp30) cc_final: 0.7721 (tp30) REVERT: q 50 GLU cc_start: 0.6934 (tm-30) cc_final: 0.5973 (tm-30) REVERT: q 54 ASP cc_start: 0.8004 (m-30) cc_final: 0.7690 (m-30) REVERT: q 81 MET cc_start: 0.8679 (mmp) cc_final: 0.8183 (mmm) REVERT: v 25 ASP cc_start: 0.8224 (t0) cc_final: 0.7553 (t0) REVERT: y 8 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8005 (mm-30) REVERT: y 31 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7427 (tm-30) REVERT: y 49 LYS cc_start: 0.8880 (tptp) cc_final: 0.8591 (tppt) outliers start: 174 outliers final: 143 residues processed: 1410 average time/residue: 1.2503 time to fit residues: 3073.6157 Evaluate side-chains 1445 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1298 time to evaluate : 6.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 68 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 109 ASP Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 30 SER Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 27 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain f residue 120 GLN Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 121 HIS Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 13 ASP Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 54 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain k residue 130 ASN Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 111 VAL Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 90 LEU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 36 ASP Chi-restraints excluded: chain o residue 42 LEU Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 111 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 49 SER Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 57 LEU Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain t residue 76 LYS Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 55 ILE Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 29 LEU Chi-restraints excluded: chain v residue 59 ILE Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 5 LEU Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 63 THR Chi-restraints excluded: chain x residue 3 ASN Chi-restraints excluded: chain x residue 36 TYR Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 604 optimal weight: 10.0000 chunk 389 optimal weight: 20.0000 chunk 583 optimal weight: 0.0570 chunk 294 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 620 optimal weight: 9.9990 chunk 665 optimal weight: 5.9990 chunk 482 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 767 optimal weight: 10.0000 overall best weight: 6.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN H 11 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 GLN J 3 GLN L 88 ASN O 15 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN f 120 GLN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 19 ASN ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN k 86 GLN k 130 ASN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** t 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 3 ASN x 70 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 157319 Z= 0.296 Angle : 0.691 59.326 235438 Z= 0.355 Chirality : 0.036 1.195 29994 Planarity : 0.006 0.129 12546 Dihedral : 23.563 179.850 78854 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.77 % Allowed : 22.37 % Favored : 73.85 % Cbeta Deviations : 0.00 % 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: 0.02 (0.11), residues: 5634 helix: 1.14 (0.12), residues: 1952 sheet: -0.33 (0.16), residues: 1061 loop : -0.63 (0.12), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 11 HIS 0.007 0.001 HIS P 14 PHE 0.025 0.002 PHE I 89 TYR 0.046 0.002 TYR s 78 ARG 0.012 0.001 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1338 time to evaluate : 6.454 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: C 5 LYS cc_start: 0.7899 (tptt) cc_final: 0.7624 (tptt) REVERT: C 121 ASP cc_start: 0.8471 (p0) cc_final: 0.8229 (p0) REVERT: F 26 MET cc_start: 0.8582 (ptm) cc_final: 0.7817 (ppp) REVERT: F 77 PHE cc_start: 0.7023 (m-80) cc_final: 0.5609 (m-10) REVERT: F 121 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8219 (p) REVERT: F 155 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8866 (p) REVERT: G 95 ARG cc_start: 0.7972 (ptm-80) cc_final: 0.7561 (ptm-80) REVERT: H 12 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8346 (pp) REVERT: L 1 MET cc_start: 0.7839 (tpp) cc_final: 0.7216 (tpt) REVERT: L 22 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7272 (tp40) REVERT: L 47 GLU cc_start: 0.7135 (pp20) cc_final: 0.6753 (pp20) REVERT: S 3 ARG cc_start: 0.6632 (ttp-110) cc_final: 0.6327 (ttp-110) REVERT: S 27 SER cc_start: 0.8870 (m) cc_final: 0.8441 (p) REVERT: T 62 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7687 (mm-30) REVERT: b 8 LYS cc_start: 0.9098 (ptmt) cc_final: 0.8407 (ptmt) REVERT: c 25 LYS cc_start: 0.8632 (tmmt) cc_final: 0.8353 (tmmt) REVERT: f 227 GLN cc_start: 0.7056 (pt0) cc_final: 0.6754 (pt0) REVERT: i 147 MET cc_start: 0.6635 (ttt) cc_final: 0.6358 (ttt) REVERT: j 1 MET cc_start: 0.6495 (tmm) cc_final: 0.6225 (tmm) REVERT: j 14 GLN cc_start: 0.8906 (mp10) cc_final: 0.8573 (mp10) REVERT: l 113 ASP cc_start: 0.8403 (p0) cc_final: 0.7936 (p0) REVERT: n 99 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8318 (mm-40) REVERT: o 32 VAL cc_start: 0.9120 (t) cc_final: 0.8765 (p) REVERT: o 34 ILE cc_start: 0.8999 (mm) cc_final: 0.8737 (mm) REVERT: o 108 THR cc_start: 0.9137 (m) cc_final: 0.8870 (p) REVERT: o 126 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8831 (mtpp) REVERT: p 62 GLU cc_start: 0.8002 (tp30) cc_final: 0.7725 (tp30) REVERT: q 50 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6125 (tm-30) REVERT: q 54 ASP cc_start: 0.7891 (m-30) cc_final: 0.7515 (m-30) REVERT: q 62 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8696 (mtmm) REVERT: q 81 MET cc_start: 0.8723 (mmp) cc_final: 0.8254 (mmp) REVERT: v 25 ASP cc_start: 0.8205 (t0) cc_final: 0.7548 (t0) REVERT: y 31 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7432 (tm-30) REVERT: y 49 LYS cc_start: 0.8898 (tptp) cc_final: 0.8609 (tppt) outliers start: 177 outliers final: 151 residues processed: 1408 average time/residue: 1.3280 time to fit residues: 3280.3776 Evaluate side-chains 1448 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1293 time to evaluate : 5.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 68 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 109 ASP Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 30 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 27 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 16 LYS Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain f residue 120 GLN Chi-restraints excluded: chain f residue 135 LEU Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 121 HIS Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 111 VAL Chi-restraints excluded: chain m residue 116 VAL Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 36 ASP Chi-restraints excluded: chain o residue 42 LEU Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 111 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 49 SER Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 62 ASN Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 57 LEU Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain t residue 76 LYS Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 55 ILE Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 29 LEU Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 59 ILE Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 63 THR Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain x residue 3 ASN Chi-restraints excluded: chain x residue 36 TYR Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 20 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 59 LYS Chi-restraints excluded: chain y residue 70 LEU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 888 optimal weight: 5.9990 chunk 935 optimal weight: 5.9990 chunk 853 optimal weight: 4.9990 chunk 909 optimal weight: 9.9990 chunk 547 optimal weight: 20.0000 chunk 396 optimal weight: 20.0000 chunk 714 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 822 optimal weight: 5.9990 chunk 860 optimal weight: 3.9990 chunk 906 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN H 33 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 89 ASN J 93 GLN L 88 ASN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN W 16 ASN Z 65 ASN f 120 GLN f 227 GLN g 19 ASN ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN k 130 ASN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 110 GLN r 66 GLN ** t 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 70 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 157319 Z= 0.250 Angle : 0.680 59.237 235438 Z= 0.350 Chirality : 0.035 1.190 29994 Planarity : 0.006 0.127 12546 Dihedral : 23.571 179.462 78854 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.65 % Allowed : 22.97 % Favored : 73.38 % 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: 0.00 (0.11), residues: 5634 helix: 1.10 (0.12), residues: 1964 sheet: -0.35 (0.16), residues: 1075 loop : -0.62 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP j 42 HIS 0.008 0.001 HIS P 14 PHE 0.021 0.002 PHE i 31 TYR 0.029 0.002 TYR i 128 ARG 0.014 0.000 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1510 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1339 time to evaluate : 6.463 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: C 5 LYS cc_start: 0.7939 (tptt) cc_final: 0.7696 (tptt) REVERT: C 121 ASP cc_start: 0.8446 (p0) cc_final: 0.8220 (p0) REVERT: C 225 MET cc_start: 0.8638 (mmt) cc_final: 0.8371 (mmt) REVERT: F 26 MET cc_start: 0.8565 (ptm) cc_final: 0.7912 (ppp) REVERT: F 77 PHE cc_start: 0.7002 (m-80) cc_final: 0.5586 (m-10) REVERT: F 121 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8236 (p) REVERT: F 155 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8865 (p) REVERT: G 95 ARG cc_start: 0.7948 (ptm-80) cc_final: 0.7565 (ptm-80) REVERT: H 12 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8309 (pp) REVERT: I 52 ASP cc_start: 0.7572 (m-30) cc_final: 0.7315 (m-30) REVERT: L 1 MET cc_start: 0.7856 (tpp) cc_final: 0.7216 (tpt) REVERT: L 22 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7264 (tp40) REVERT: L 47 GLU cc_start: 0.7080 (pp20) cc_final: 0.6738 (pp20) REVERT: R 42 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7038 (ptmt) REVERT: S 3 ARG cc_start: 0.6614 (ttp-110) cc_final: 0.6275 (ttp-110) REVERT: S 27 SER cc_start: 0.8855 (m) cc_final: 0.8450 (p) REVERT: T 27 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8308 (p0) REVERT: Y 11 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7389 (mmm160) REVERT: b 8 LYS cc_start: 0.9020 (ptmt) cc_final: 0.8331 (ptmt) REVERT: c 25 LYS cc_start: 0.8639 (tmmt) cc_final: 0.8365 (tmmt) REVERT: f 227 GLN cc_start: 0.7120 (pt0) cc_final: 0.6790 (pt0) REVERT: i 147 MET cc_start: 0.6603 (ttt) cc_final: 0.6348 (ttt) REVERT: l 90 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7099 (p0) REVERT: l 113 ASP cc_start: 0.8357 (p0) cc_final: 0.7971 (p0) REVERT: o 32 VAL cc_start: 0.9118 (t) cc_final: 0.8777 (p) REVERT: o 34 ILE cc_start: 0.8962 (mm) cc_final: 0.8694 (mm) REVERT: o 126 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8827 (mtpp) REVERT: q 50 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6195 (tm-30) REVERT: q 54 ASP cc_start: 0.7893 (m-30) cc_final: 0.7492 (m-30) REVERT: q 81 MET cc_start: 0.8669 (mmp) cc_final: 0.7952 (mmp) REVERT: v 25 ASP cc_start: 0.8113 (t0) cc_final: 0.7476 (t0) REVERT: y 31 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7418 (tm-30) REVERT: y 49 LYS cc_start: 0.8864 (tptp) cc_final: 0.8583 (tppt) outliers start: 171 outliers final: 152 residues processed: 1409 average time/residue: 1.2580 time to fit residues: 3089.4995 Evaluate side-chains 1460 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1301 time to evaluate : 6.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 68 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain R residue 42 LYS Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 109 ASP Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 27 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 16 LYS Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain f residue 120 GLN Chi-restraints excluded: chain f residue 135 LEU Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 121 HIS Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 13 ASP Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 54 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain k residue 130 ASN Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 111 VAL Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 36 ASP Chi-restraints excluded: chain o residue 42 LEU Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 111 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 49 SER Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 57 LEU Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain t residue 76 LYS Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 55 ILE Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 29 LEU Chi-restraints excluded: chain v residue 59 ILE Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 63 THR Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain x residue 36 TYR Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 20 LYS Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 59 LYS Chi-restraints excluded: chain y residue 60 LEU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 597 optimal weight: 5.9990 chunk 962 optimal weight: 30.0000 chunk 587 optimal weight: 0.6980 chunk 456 optimal weight: 4.9990 chunk 668 optimal weight: 0.8980 chunk 1009 optimal weight: 3.9990 chunk 928 optimal weight: 6.9990 chunk 803 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 620 optimal weight: 6.9990 chunk 492 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN J 3 GLN J 89 ASN L 88 ASN O 15 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN W 16 ASN Z 65 ASN ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 19 ASN ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN k 130 ASN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 99 GLN ** t 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 70 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.328 157319 Z= 0.250 Angle : 0.728 59.202 235438 Z= 0.384 Chirality : 0.035 1.187 29994 Planarity : 0.006 0.158 12546 Dihedral : 23.575 179.456 78854 Min Nonbonded Distance : 1.119 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % Rotamer: Outliers : 3.69 % Allowed : 23.16 % Favored : 73.15 % Cbeta Deviations : 0.04 % 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: 0.00 (0.11), residues: 5634 helix: 1.10 (0.12), residues: 1964 sheet: -0.34 (0.16), residues: 1073 loop : -0.63 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP j 42 HIS 0.011 0.001 HIS j 11 PHE 0.020 0.002 PHE i 31 TYR 0.026 0.002 TYR I 44 ARG 0.013 0.000 ARG G 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1484 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1311 time to evaluate : 6.426 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: C 5 LYS cc_start: 0.7936 (tptt) cc_final: 0.7689 (tptt) REVERT: C 18 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7709 (tptt) REVERT: C 121 ASP cc_start: 0.8443 (p0) cc_final: 0.8218 (p0) REVERT: C 225 MET cc_start: 0.8631 (mmt) cc_final: 0.8355 (mmt) REVERT: F 26 MET cc_start: 0.8558 (ptm) cc_final: 0.7935 (ppp) REVERT: F 77 PHE cc_start: 0.6997 (m-80) cc_final: 0.5582 (m-10) REVERT: F 121 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8229 (p) REVERT: F 155 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8863 (p) REVERT: G 95 ARG cc_start: 0.7940 (ptm-80) cc_final: 0.7560 (ptm-80) REVERT: H 12 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8305 (pp) REVERT: L 1 MET cc_start: 0.7850 (tpp) cc_final: 0.7215 (tpt) REVERT: L 22 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7261 (tp40) REVERT: L 47 GLU cc_start: 0.7061 (pp20) cc_final: 0.6736 (pp20) REVERT: R 42 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7032 (ptmt) REVERT: S 3 ARG cc_start: 0.6609 (ttp-110) cc_final: 0.6266 (ttp-110) REVERT: S 27 SER cc_start: 0.8863 (m) cc_final: 0.8447 (p) REVERT: T 27 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8305 (p0) REVERT: b 8 LYS cc_start: 0.9022 (ptmt) cc_final: 0.8346 (ptmt) REVERT: c 25 LYS cc_start: 0.8631 (tmmt) cc_final: 0.8359 (tmmt) REVERT: f 227 GLN cc_start: 0.7126 (pt0) cc_final: 0.6859 (pt0) REVERT: i 147 MET cc_start: 0.6603 (ttt) cc_final: 0.6350 (ttt) REVERT: l 90 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7091 (p0) REVERT: l 113 ASP cc_start: 0.8369 (p0) cc_final: 0.7969 (p0) REVERT: o 32 VAL cc_start: 0.9111 (t) cc_final: 0.8773 (p) REVERT: o 34 ILE cc_start: 0.8954 (mm) cc_final: 0.8687 (mm) REVERT: o 126 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8825 (mtpp) REVERT: q 50 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6183 (tm-30) REVERT: q 54 ASP cc_start: 0.7889 (m-30) cc_final: 0.7470 (m-30) REVERT: q 81 MET cc_start: 0.8668 (mmp) cc_final: 0.7950 (mmp) REVERT: v 25 ASP cc_start: 0.8114 (t0) cc_final: 0.7459 (t0) REVERT: w 47 LEU cc_start: 0.8508 (mp) cc_final: 0.8302 (mt) REVERT: y 31 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7407 (tm-30) REVERT: y 49 LYS cc_start: 0.8859 (tptp) cc_final: 0.8576 (tppt) REVERT: y 70 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5635 (mm) outliers start: 173 outliers final: 156 residues processed: 1380 average time/residue: 1.2521 time to fit residues: 3014.1625 Evaluate side-chains 1459 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1294 time to evaluate : 6.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 136 MET Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 68 GLU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain R residue 42 LYS Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 109 ASP Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 30 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 27 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 12 LYS Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 16 LYS Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain e residue 12 ARG Chi-restraints excluded: chain f residue 120 GLN Chi-restraints excluded: chain f residue 135 LEU Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 138 SER Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 115 LEU Chi-restraints excluded: chain i residue 121 HIS Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 10 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 54 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 62 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 61 LEU Chi-restraints excluded: chain m residue 96 SER Chi-restraints excluded: chain m residue 111 VAL Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain n residue 17 LEU Chi-restraints excluded: chain n residue 76 ILE Chi-restraints excluded: chain n residue 101 SER Chi-restraints excluded: chain o residue 26 SER Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 36 ASP Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 111 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 49 SER Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 104 THR Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 57 LEU Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain t residue 76 LYS Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 55 ILE Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 29 LEU Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 59 ILE Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 63 THR Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain x residue 3 ASN Chi-restraints excluded: chain x residue 36 TYR Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain y residue 9 ASN Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 20 LYS Chi-restraints excluded: chain y residue 59 LYS Chi-restraints excluded: chain y residue 60 LEU Chi-restraints excluded: chain y residue 70 LEU Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 638 optimal weight: 30.0000 chunk 856 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 740 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 804 optimal weight: 5.9990 chunk 336 optimal weight: 30.0000 chunk 826 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN J 3 GLN ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN O 56 HIS ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN ** X 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 ASN ** b 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 19 ASN ** g 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 99 GLN ** t 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 70 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.042480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034438 restraints weight = 937129.898| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.84 r_work: 0.2641 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.328 157319 Z= 0.250 Angle : 0.728 59.202 235438 Z= 0.384 Chirality : 0.035 1.187 29994 Planarity : 0.006 0.158 12546 Dihedral : 23.575 179.456 78854 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % Rotamer: Outliers : 3.52 % Allowed : 23.37 % Favored : 73.11 % Cbeta Deviations : 0.04 % 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: 0.00 (0.11), residues: 5634 helix: 1.10 (0.12), residues: 1964 sheet: -0.34 (0.16), residues: 1073 loop : -0.63 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP j 42 HIS 0.011 0.001 HIS j 11 PHE 0.020 0.002 PHE i 31 TYR 0.026 0.002 TYR I 44 ARG 0.013 0.000 ARG G 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46328.69 seconds wall clock time: 804 minutes 35.92 seconds (48275.92 seconds total)