Starting phenix.real_space_refine on Sun Mar 24 02:09:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3l_15116/03_2024/8a3l_15116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3l_15116/03_2024/8a3l_15116.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3l_15116/03_2024/8a3l_15116_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3l_15116/03_2024/8a3l_15116_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3l_15116/03_2024/8a3l_15116_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3l_15116/03_2024/8a3l_15116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3l_15116/03_2024/8a3l_15116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3l_15116/03_2024/8a3l_15116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a3l_15116/03_2024/8a3l_15116_updated.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4720 5.49 5 Mg 313 5.21 5 S 150 5.16 5 C 74016 2.51 5 N 27438 2.21 5 O 41001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "R ARG 12": "NH1" <-> "NH2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "U GLU 39": "OE1" <-> "OE2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "Y GLU 11": "OE1" <-> "OE2" Residue "Y GLU 15": "OE1" <-> "OE2" Residue "Y ARG 19": "NH1" <-> "NH2" Residue "Y GLU 76": "OE1" <-> "OE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ARG 128": "NH1" <-> "NH2" Residue "Y ARG 142": "NH1" <-> "NH2" Residue "Y GLU 151": "OE1" <-> "OE2" Residue "Y GLU 175": "OE1" <-> "OE2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g GLU 167": "OE1" <-> "OE2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h GLU 87": "OE1" <-> "OE2" Residue "h GLU 127": "OE1" <-> "OE2" Residue "i PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i GLU 102": "OE1" <-> "OE2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "j GLU 106": "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 106": "OE1" <-> "OE2" Residue "k GLU 115": "OE1" <-> "OE2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l ARG 169": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "q PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 2": "OE1" <-> "OE2" Residue "r GLU 78": "OE1" <-> "OE2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t GLU 10": "OE1" <-> "OE2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 13": "OE1" <-> "OE2" 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 "y GLU 59": "OE1" <-> "OE2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ARG 52": "NH1" <-> "NH2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 13": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147640 Number of models: 1 Model: "" Number of chains: 65 Chain: "A" Number of atoms: 33022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33022 Classifications: {'RNA': 1539} Modifications used: {'rna2p': 1, 'rna2p_pur': 96, 'rna2p_pyr': 66, 'rna3p': 10, 'rna3p_pur': 770, 'rna3p_pyr': 596} Link IDs: {'rna2p': 163, 'rna3p': 1375} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" 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: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 569 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "V" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p': 3, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 7, 'rna3p': 69} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "W" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "X" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 136 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 5} Chain: "Y" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1332 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "a" Number of atoms: 62337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62337 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 7, 'rna2p_pur': 224, 'rna2p_pyr': 106, 'rna3p': 17, 'rna3p_pur': 1444, 'rna3p_pyr': 1105} Link IDs: {'rna2p': 337, 'rna3p': 2565} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 59, 'rna3p_pyr': 52} Link IDs: {'rna2p': 9, 'rna3p': 110} 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: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} 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: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 137 " Not linked: pdbres="MS6 l 137 " pdbres="GLY l 138 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "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: {'PCIS': 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: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "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: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" 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: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" 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: "2" 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: "3" 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: "4" 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Unusual residues: {' MG': 71} Classifications: {'undetermined': 71} Link IDs: {None: 70} Chain: "a" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 234 Unusual residues: {' MG': 234} Classifications: {'undetermined': 234} Link IDs: {None: 233} Chain: "b" 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: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0ZY2 SG CYS 3 11 48.503 101.172 138.712 1.00 93.48 S ATOM A0ZYR SG CYS 3 14 50.090 102.763 135.621 1.00 91.31 S ATOM A101M SG CYS 3 27 47.740 104.783 137.817 1.00 91.58 S ATOM A107P SG CYS 4 16 122.465 21.488 158.144 1.00117.99 S ATOM A1081 SG CYS 4 18 120.255 18.522 159.194 1.00119.43 S ATOM A10BZ SG CYS 4 37 119.261 20.685 156.321 1.00116.98 S ATOM A10CK SG CYS 4 40 119.156 22.057 159.916 1.00116.45 S Time building chain proxies: 58.23, per 1000 atoms: 0.39 Number of scatterers: 147640 At special positions: 0 Unit cell: (231.287, 244.682, 266.114, 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 4720 15.00 Mg 313 11.99 O 41001 8.00 N 27438 7.00 C 74016 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 65.45 Conformation dependent library (CDL) restraints added in 8.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " Number of angles added : 9 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10794 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: 169 helices and 75 sheets defined 37.5% alpha, 19.9% beta 1527 base pairs and 2447 stacking pairs defined. Time for finding SS restraints: 77.03 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.774A pdb=" N ILE B 31 " --> pdb=" O MET B 27 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 44 through 64 Proline residue: B 48 - end of helix removed outlier: 3.626A pdb=" N GLU B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA B 53 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.718A pdb=" N LYS B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 123 removed outlier: 4.964A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 removed outlier: 3.626A pdb=" N ALA B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 207 through 227 removed outlier: 3.969A pdb=" N LEU B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.990A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.546A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.145A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.707A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 4.151A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.251A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.718A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.734A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.427A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.578A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 5.137A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 4.355A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 4.106A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 147 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 11 through 16 removed outlier: 3.870A pdb=" N SER F 15 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLU F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 11 through 16' Processing helix chain 'F' and resid 17 through 33 Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.527A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 Processing helix chain 'G' and resid 115 through 130 removed outlier: 3.656A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 153 removed outlier: 5.131A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS G 153 " --> pdb=" O LYS G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 92 through 102 removed outlier: 5.001A pdb=" N SER I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.861A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.684A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.160A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 75 removed outlier: 3.626A pdb=" N LYS K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 104 removed outlier: 4.159A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.671A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.573A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 64 removed outlier: 3.519A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 52 Proline residue: N 52 - end of helix Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 44 removed outlier: 4.175A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.586A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.826A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 4.122A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 66 removed outlier: 5.345A pdb=" N GLN R 52 " --> pdb=" O ARG R 48 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.297A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.636A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 removed outlier: 3.808A pdb=" N GLY U 27 " --> pdb=" O CYS U 23 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 38 removed outlier: 3.939A pdb=" N ARG U 34 " --> pdb=" O ALA U 30 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR U 38 " --> pdb=" O ARG U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 68 removed outlier: 5.185A pdb=" N ARG U 45 " --> pdb=" O PRO U 41 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG U 55 " --> pdb=" O SER U 51 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LYS U 59 " --> pdb=" O ARG U 55 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU U 60 " --> pdb=" O HIS U 56 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG U 62 " --> pdb=" O LYS U 58 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU U 63 " --> pdb=" O LYS U 59 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN U 64 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG U 66 " --> pdb=" O ARG U 62 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 19 removed outlier: 3.705A pdb=" N PHE Y 9 " --> pdb=" O PHE Y 5 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU Y 11 " --> pdb=" O GLN Y 7 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR Y 18 " --> pdb=" O LYS Y 14 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG Y 19 " --> pdb=" O GLU Y 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 17 removed outlier: 4.852A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL c 16 " --> pdb=" O GLY c 12 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL c 17 " --> pdb=" O ARG c 13 " (cutoff:3.500A) 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: 3.658A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY c 215 " --> pdb=" O ALA c 211 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.894A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.267A 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: 4.744A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'c' and resid 197 through 202 removed outlier: 4.144A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.687A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.436A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.270A 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: 5.477A pdb=" N GLN e 41 " --> pdb=" O ALA e 37 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.303A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (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: 4.683A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 5.094A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 47 removed outlier: 3.521A pdb=" N ASP f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 62 Processing helix chain 'f' and resid 93 through 112 removed outlier: 4.680A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix removed outlier: 5.853A pdb=" N ARG f 112 " --> pdb=" O VAL f 108 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.528A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 removed outlier: 3.656A pdb=" N ILE f 137 " --> pdb=" O GLU f 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE f 138 " --> pdb=" O GLN f 135 " (cutoff:3.500A) Proline residue: f 139 - end of helix No H-bonds generated for 'chain 'f' and resid 134 through 139' Processing helix chain 'g' and resid 2 through 7 Processing helix chain 'g' and resid 60 through 81 removed outlier: 5.147A pdb=" N GLN g 64 " --> pdb=" O ASP g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 4.088A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 29 Processing helix chain 'h' and resid 40 through 50 removed outlier: 3.948A pdb=" N GLU h 45 " --> pdb=" O LYS h 41 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE h 47 " --> pdb=" O ASN h 43 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU h 48 " --> pdb=" O ILE h 44 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG h 50 " --> pdb=" O PHE h 46 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 73 removed outlier: 4.244A pdb=" N ALA h 59 " --> pdb=" O GLU h 55 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU h 62 " --> pdb=" O LEU h 58 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA h 64 " --> pdb=" O GLU h 60 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG h 68 " --> pdb=" O ALA h 64 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA h 69 " --> pdb=" O ALA h 65 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU h 70 " --> pdb=" O ASN h 66 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS h 71 " --> pdb=" O ALA h 67 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 107 removed outlier: 3.677A pdb=" N ALA h 105 " --> pdb=" O ASP h 101 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA h 106 " --> pdb=" O ALA h 102 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY h 107 " --> pdb=" O VAL h 103 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.991A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.213A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 123 removed outlier: 3.810A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) removed outlier: 5.901A 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 56 through 62 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 3.859A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.698A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.887A 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 164 through 180 removed outlier: 3.950A pdb=" N LYS l 178 " --> pdb=" O LEU l 174 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU l 179 " --> pdb=" O ALA l 175 " (cutoff:3.500A) Proline residue: l 180 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 58 removed outlier: 4.552A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.172A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 4.294A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.567A 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: 4.541A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 4.837A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.078A 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: 3.825A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 5.032A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 Processing helix chain 'p' and resid 26 through 31 removed outlier: 4.125A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.890A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 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: 3.847A pdb=" N LEU r 19 " --> pdb=" O GLN r 15 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 Processing helix chain 'r' and resid 41 through 61 Processing helix chain 's' and resid 3 through 11 removed outlier: 4.050A 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 51 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.812A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.530A 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: 4.229A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 4.489A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) 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: 3.881A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 removed outlier: 3.608A pdb=" N GLY x 35 " --> pdb=" O GLN x 31 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.715A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (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 9 through 21 removed outlier: 4.683A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP z 20 " --> pdb=" O ARG z 16 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA z 21 " --> pdb=" O ARG z 17 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.313A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 32 through 37 removed outlier: 4.855A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 52 through 63 removed outlier: 4.058A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 65 removed outlier: 4.406A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.842A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE B 41 " --> pdb=" O HIS B 15 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 89 through 93 removed outlier: 3.536A pdb=" N ILE B 164 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 54 through 59 Processing sheet with id= 4, first strand: chain 'C' and resid 164 through 169 removed outlier: 6.541A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLU C 206 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG C 179 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 140 through 144 removed outlier: 4.099A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N TRP D 170 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.759A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 83 through 88 removed outlier: 7.460A pdb=" N HIS E 83 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 33 through 41 removed outlier: 6.857A pdb=" N ARG E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.551A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.817A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.672A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.142A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 74 through 77 removed outlier: 4.611A pdb=" N SER H 74 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 5 through 11 removed outlier: 4.106A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.115A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 44 through 53 removed outlier: 8.345A pdb=" N ALA J 61 " --> pdb=" O ILE J 53 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'K' and resid 29 through 36 removed outlier: 3.812A pdb=" N ASN K 29 " --> pdb=" O SER K 26 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.140A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 36 through 41 removed outlier: 4.845A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.511A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Q' and resid 7 through 11 removed outlier: 7.163A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'S' and resid 30 through 34 removed outlier: 4.387A pdb=" N LEU S 47 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Y' and resid 35 through 39 removed outlier: 3.953A pdb=" N VAL Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE Y 48 " --> pdb=" O VAL Y 36 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL Y 38 " --> pdb=" O SER Y 46 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Y' and resid 153 through 156 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'c' and resid 33 through 36 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'c' and resid 80 through 83 removed outlier: 6.854A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'c' and resid 138 through 142 removed outlier: 3.964A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.506A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'd' and resid 3 through 6 removed outlier: 4.184A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.640A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'd' and resid 36 through 40 removed outlier: 3.516A pdb=" N GLN d 36 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU d 40 " --> pdb=" O TYR d 45 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR d 45 " --> pdb=" O LEU d 40 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'd' and resid 46 through 51 removed outlier: 5.779A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.227A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'e' and resid 1 through 6 removed outlier: 3.719A pdb=" N MET e 1 " --> pdb=" O VAL e 14 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU e 5 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'e' and resid 42 through 46 removed outlier: 4.427A pdb=" N GLY e 42 " --> pdb=" O GLN e 90 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG e 44 " --> pdb=" O ARG e 88 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG e 88 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLN e 46 " --> pdb=" O ALA e 86 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA e 86 " --> pdb=" O GLN e 46 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.582A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'f' and resid 65 through 69 removed outlier: 5.219A pdb=" N ILE f 85 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'g' and resid 8 through 11 removed outlier: 3.741A pdb=" N LEU g 50 " --> pdb=" O VAL g 9 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN g 48 " --> pdb=" O VAL g 11 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ALA g 46 " --> pdb=" O THR g 49 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR g 51 " --> pdb=" O LYS g 44 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA g 40 " --> pdb=" O ARG g 55 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'g' and resid 15 through 20 removed outlier: 6.042A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'g' and resid 94 through 99 removed outlier: 6.982A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'g' and resid 121 through 125 removed outlier: 6.232A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'h' and resid 2 through 6 removed outlier: 5.480A pdb=" N GLN h 2 " --> pdb=" O ALA h 39 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS h 35 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'h' and resid 76 through 81 removed outlier: 5.810A pdb=" N GLU h 76 " --> pdb=" O LYS h 141 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE h 143 " --> pdb=" O GLU h 76 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL h 147 " --> pdb=" O ILE h 80 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU h 114 " --> pdb=" O GLN h 133 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'i' and resid 52 through 57 removed outlier: 5.366A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.602A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'j' and resid 18 through 21 removed outlier: 4.240A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.805A pdb=" N TYR l 158 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU l 33 " --> pdb=" O LEU l 157 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS l 155 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.841A pdb=" N SER l 30 " --> pdb=" O LYS l 188 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS l 182 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.486A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'n' and resid 49 through 52 Processing sheet with id= 53, first strand: chain 'o' and resid 49 through 53 removed outlier: 3.707A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG o 53 " --> pdb=" O HIS o 56 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'o' and resid 57 through 64 removed outlier: 7.637A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 11 through 14 Processing sheet with id= 56, first strand: chain 'q' and resid 17 through 21 removed outlier: 4.284A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 58, first strand: chain 'q' and resid 64 through 68 Processing sheet with id= 59, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.077A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'r' and resid 1 through 8 removed outlier: 7.072A pdb=" N MET r 1 " --> pdb=" O ASP r 109 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP r 109 " --> pdb=" O MET r 1 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL r 106 " --> pdb=" O THR r 72 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'r' and resid 81 through 88 removed outlier: 4.344A pdb=" N ARG r 92 " --> pdb=" O ARG r 88 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 's' and resid 28 through 33 removed outlier: 6.281A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 't' and resid 40 through 49 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain 't' and resid 83 through 87 Processing sheet with id= 65, first strand: chain 'u' and resid 69 through 72 removed outlier: 3.791A pdb=" N GLU u 7 " --> pdb=" O GLU u 41 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.194A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'v' and resid 66 through 71 Processing sheet with id= 68, first strand: chain 'w' and resid 12 through 19 removed outlier: 4.581A pdb=" N ASN w 23 " --> pdb=" O SER w 19 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'w' and resid 35 through 41 Processing sheet with id= 70, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.062A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.414A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '0' and resid 19 through 24 removed outlier: 6.056A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '2' and resid 22 through 25 removed outlier: 5.365A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '3' and resid 14 through 19 Processing sheet with id= 75, first strand: chain '4' and resid 20 through 25 1942 hydrogen bonds defined for protein. 5745 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3860 hydrogen bonds 6070 hydrogen bond angles 0 basepair planarities 1527 basepair parallelities 2447 stacking parallelities Total time for adding SS restraints: 276.67 Time building geometry restraints manager: 70.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 11987 1.27 - 1.41: 52690 1.41 - 1.54: 85670 1.54 - 1.68: 9482 1.68 - 1.81: 265 Bond restraints: 160094 Sorted by residual: bond pdb=" C4 5MU V 55 " pdb=" C5 5MU V 55 " ideal model delta sigma weight residual 1.802 1.477 0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.483 0.319 2.00e-02 2.50e+03 2.55e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.483 0.319 2.00e-02 2.50e+03 2.55e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.340 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" N1 5MU V 55 " pdb=" C6 5MU V 55 " ideal model delta sigma weight residual 1.635 1.342 0.293 2.00e-02 2.50e+03 2.15e+02 ... (remaining 160089 not shown) Histogram of bond angle deviations from ideal: 96.89 - 105.00: 21887 105.00 - 113.12: 98530 113.12 - 121.23: 77927 121.23 - 129.35: 37346 129.35 - 137.46: 3835 Bond angle restraints: 239525 Sorted by residual: angle pdb=" N ASN U 64 " pdb=" CA ASN U 64 " pdb=" C ASN U 64 " ideal model delta sigma weight residual 113.18 97.66 15.52 1.21e+00 6.83e-01 1.65e+02 angle pdb=" C HIS B 15 " pdb=" N PHE B 16 " pdb=" CA PHE B 16 " ideal model delta sigma weight residual 122.64 101.03 21.61 1.70e+00 3.46e-01 1.62e+02 angle pdb=" N SER Y 12 " pdb=" CA SER Y 12 " pdb=" C SER Y 12 " ideal model delta sigma weight residual 112.89 98.52 14.37 1.24e+00 6.50e-01 1.34e+02 angle pdb=" N GLN Y 7 " pdb=" CA GLN Y 7 " pdb=" C GLN Y 7 " ideal model delta sigma weight residual 112.23 102.15 10.08 1.26e+00 6.30e-01 6.40e+01 angle pdb=" N LEU B 43 " pdb=" CA LEU B 43 " pdb=" C LEU B 43 " ideal model delta sigma weight residual 113.38 104.34 9.04 1.17e+00 7.31e-01 5.97e+01 ... (remaining 239520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 89839 35.82 - 71.65: 11240 71.65 - 107.47: 1326 107.47 - 143.29: 32 143.29 - 179.11: 30 Dihedral angle restraints: 102467 sinusoidal: 85737 harmonic: 16730 Sorted by residual: dihedral pdb=" C4' C a1489 " pdb=" C3' C a1489 " pdb=" C2' C a1489 " pdb=" C1' C a1489 " ideal model delta sinusoidal sigma weight residual -35.00 34.37 -69.37 1 8.00e+00 1.56e-02 9.71e+01 dihedral pdb=" C5' C a1489 " pdb=" C4' C a1489 " pdb=" C3' C a1489 " pdb=" O3' C a1489 " ideal model delta sinusoidal sigma weight residual 147.00 78.73 68.27 1 8.00e+00 1.56e-02 9.45e+01 dihedral pdb=" C5' G A1347 " pdb=" C4' G A1347 " pdb=" C3' G A1347 " pdb=" O3' G A1347 " ideal model delta sinusoidal sigma weight residual 147.00 79.90 67.10 1 8.00e+00 1.56e-02 9.16e+01 ... (remaining 102464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 28700 0.091 - 0.182: 1565 0.182 - 0.273: 226 0.273 - 0.364: 25 0.364 - 0.455: 5 Chirality restraints: 30521 Sorted by residual: chirality pdb=" C3' G a 372 " pdb=" C4' G a 372 " pdb=" O3' G a 372 " pdb=" C2' G a 372 " both_signs ideal model delta sigma weight residual False -2.74 -2.29 -0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" C3' G A1300 " pdb=" C4' G A1300 " pdb=" O3' G A1300 " pdb=" C2' G A1300 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" C3' G A1347 " pdb=" C4' G A1347 " pdb=" O3' G A1347 " pdb=" C2' G A1347 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 30518 not shown) Planarity restraints: 12814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " -0.040 2.00e-02 2.50e+03 6.14e-01 8.49e+03 pdb=" C4' OMC a2498 " -0.468 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " -0.764 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " 0.586 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " 0.610 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " 0.215 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " -0.918 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " -0.196 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " 0.974 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.047 2.00e-02 2.50e+03 5.98e-01 8.03e+03 pdb=" C4' 2MG A1516 " 0.497 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.742 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.525 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.580 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.195 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.866 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.224 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.981 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " -0.009 2.00e-02 2.50e+03 5.93e-01 7.92e+03 pdb=" C4' 2MG A1207 " 0.487 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " 0.701 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " -0.558 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " -0.600 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " -0.192 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " 0.886 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " 0.232 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " -0.945 2.00e-02 2.50e+03 ... (remaining 12811 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 387 2.27 - 2.92: 59151 2.92 - 3.58: 236910 3.58 - 4.24: 463185 4.24 - 4.90: 623578 Nonbonded interactions: 1383211 Sorted by model distance: nonbonded pdb=" CE1 HIS B 18 " pdb=" CE1 PHE Y 79 " model vdw 1.607 3.560 nonbonded pdb=" O2 PSU a 746 " pdb="MG MG a3088 " model vdw 1.611 2.170 nonbonded pdb=" OP2 2MA a2503 " pdb="MG MG a3145 " model vdw 1.706 2.170 nonbonded pdb=" OP2 C A1098 " pdb=" NZ LYS B 143 " model vdw 1.765 2.520 nonbonded pdb=" O2 U A1540 " pdb=" C2 A X 1 " model vdw 1.807 3.340 ... (remaining 1383206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'V' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name O2' or name C1' or name N1 or name C2 or \ name O2 or name N3 or name C4 or name N4 or name C5 or name C6 )) or resid 2 thr \ ough 7 or resid 9 through 20 or resid 22 through 46 or resid 48 through 54 or re \ sid 57 through 77)) selection = (chain 'W' and (resid 1 through 7 or resid 9 through 20 or resid 22 through 46 o \ r resid 48 through 54 or resid 57 through 77)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.240 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: 0.150 Extract box with map and model: 28.190 Check model and map are aligned: 1.660 Set scattering table: 1.060 Process input model: 613.940 Find NCS groups from input model: 3.340 Set up NCS constraints: 0.500 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: 0.040 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 658.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.325 160094 Z= 0.458 Angle : 0.760 21.606 239525 Z= 0.425 Chirality : 0.047 0.455 30521 Planarity : 0.019 0.614 12814 Dihedral : 23.475 179.115 91673 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.47 % Favored : 91.88 % Rotamer: Outliers : 2.12 % Allowed : 0.83 % Favored : 97.04 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.12 % 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: -0.87 (0.11), residues: 5767 helix: 0.62 (0.12), residues: 1850 sheet: -0.78 (0.16), residues: 1066 loop : -1.28 (0.11), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 23 HIS 0.032 0.002 HIS l 13 PHE 0.026 0.002 PHE 4 64 TYR 0.018 0.002 TYR f 128 ARG 0.007 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1614 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1512 time to evaluate : 6.538 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: B 23 TRP cc_start: 0.7369 (p-90) cc_final: 0.7071 (p-90) REVERT: C 114 LYS cc_start: 0.7990 (tptt) cc_final: 0.7762 (tptp) REVERT: C 162 ILE cc_start: 0.8448 (mt) cc_final: 0.8018 (pt) REVERT: C 187 SER cc_start: 0.8704 (t) cc_final: 0.8334 (m) REVERT: D 46 PRO cc_start: 0.6546 (Cg_endo) cc_final: 0.6205 (Cg_exo) REVERT: D 91 LEU cc_start: 0.7924 (mt) cc_final: 0.7670 (mt) REVERT: E 31 PHE cc_start: 0.7418 (m-80) cc_final: 0.7205 (m-80) REVERT: E 66 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8295 (mtpt) REVERT: E 86 LYS cc_start: 0.8510 (mttm) cc_final: 0.8269 (mttp) REVERT: E 88 VAL cc_start: 0.8613 (t) cc_final: 0.8291 (m) REVERT: E 96 MET cc_start: 0.8438 (mtm) cc_final: 0.8175 (mtm) REVERT: E 97 GLN cc_start: 0.8260 (tt0) cc_final: 0.7967 (tt0) REVERT: E 131 THR cc_start: 0.8678 (p) cc_final: 0.8453 (p) REVERT: F 9 MET cc_start: 0.7924 (ptm) cc_final: 0.7688 (ptp) REVERT: F 45 ARG cc_start: 0.7375 (mtp85) cc_final: 0.7163 (mtp85) REVERT: F 80 PHE cc_start: 0.8064 (m-10) cc_final: 0.7861 (m-80) REVERT: F 96 VAL cc_start: 0.8381 (t) cc_final: 0.8151 (t) REVERT: G 58 GLU cc_start: 0.8530 (mp0) cc_final: 0.8144 (mp0) REVERT: G 74 GLU cc_start: 0.7838 (pt0) cc_final: 0.7621 (pt0) REVERT: G 130 ASN cc_start: 0.7396 (m-40) cc_final: 0.7166 (m110) REVERT: G 139 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7178 (mm-30) REVERT: H 38 ASN cc_start: 0.7481 (m-40) cc_final: 0.6965 (m-40) REVERT: H 50 LYS cc_start: 0.7358 (ptmt) cc_final: 0.7141 (ptmm) REVERT: H 69 LYS cc_start: 0.7023 (mtpt) cc_final: 0.6786 (pttm) REVERT: H 94 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7846 (mmtp) REVERT: I 111 VAL cc_start: 0.8309 (m) cc_final: 0.8109 (p) REVERT: I 112 GLU cc_start: 0.7154 (tt0) cc_final: 0.6660 (tt0) REVERT: J 14 ASP cc_start: 0.6583 (t0) cc_final: 0.5988 (t0) REVERT: K 18 ASP cc_start: 0.6853 (m-30) cc_final: 0.6580 (p0) REVERT: L 43 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7348 (mtpp) REVERT: L 80 ILE cc_start: 0.8090 (pt) cc_final: 0.7882 (pt) REVERT: L 115 SER cc_start: 0.8940 (p) cc_final: 0.8595 (p) REVERT: M 39 ILE cc_start: 0.7376 (mt) cc_final: 0.7168 (tt) REVERT: N 6 MET cc_start: 0.8224 (mmm) cc_final: 0.7972 (mmt) REVERT: O 81 LEU cc_start: 0.8756 (tp) cc_final: 0.8386 (tt) REVERT: P 26 ASN cc_start: 0.8882 (m-40) cc_final: 0.8617 (m-40) REVERT: R 16 GLU cc_start: 0.3298 (OUTLIER) cc_final: 0.2424 (tp30) REVERT: S 34 TRP cc_start: 0.7673 (m-90) cc_final: 0.7040 (m-90) REVERT: S 71 LEU cc_start: 0.8966 (mp) cc_final: 0.8742 (mt) REVERT: T 8 LYS cc_start: 0.7587 (mttt) cc_final: 0.7300 (mtmm) REVERT: T 18 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7842 (ttp80) REVERT: T 19 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7669 (mtmm) REVERT: T 70 ASN cc_start: 0.8022 (m-40) cc_final: 0.7442 (m110) REVERT: U 33 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7599 (mtt-85) REVERT: U 35 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7834 (mtp85) REVERT: U 44 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: U 58 LYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5065 (pttp) REVERT: U 63 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5491 (tm-30) REVERT: U 68 THR cc_start: 0.4139 (OUTLIER) cc_final: 0.3631 (p) REVERT: Y 120 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: Y 154 PHE cc_start: 0.5460 (OUTLIER) cc_final: 0.5183 (p90) REVERT: c 28 LYS cc_start: 0.8306 (mmtm) cc_final: 0.8053 (mmtp) REVERT: c 36 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7949 (ttmt) REVERT: c 70 ASN cc_start: 0.7063 (m-40) cc_final: 0.6822 (m-40) REVERT: c 216 VAL cc_start: 0.9376 (t) cc_final: 0.9082 (p) REVERT: e 132 LYS cc_start: 0.7484 (ttpp) cc_final: 0.7232 (ptmt) REVERT: e 184 ASP cc_start: 0.7054 (t0) cc_final: 0.6283 (m-30) REVERT: f 61 SER cc_start: 0.7378 (m) cc_final: 0.7152 (p) REVERT: f 88 LYS cc_start: 0.7942 (pttp) cc_final: 0.7484 (pttm) REVERT: f 136 ILE cc_start: 0.8383 (pt) cc_final: 0.8168 (pt) REVERT: g 25 THR cc_start: 0.5519 (m) cc_final: 0.5220 (p) REVERT: i 16 TYR cc_start: 0.8145 (m-80) cc_final: 0.7614 (m-80) REVERT: i 108 MET cc_start: 0.8936 (mtt) cc_final: 0.8620 (mtt) REVERT: i 118 MET cc_start: 0.7663 (mtt) cc_final: 0.7414 (mtt) REVERT: j 47 ILE cc_start: 0.7492 (pt) cc_final: 0.6814 (pt) REVERT: j 56 ASP cc_start: 0.7324 (m-30) cc_final: 0.7009 (m-30) REVERT: j 73 ASP cc_start: 0.7990 (p0) cc_final: 0.7765 (p0) REVERT: j 97 THR cc_start: 0.7565 (p) cc_final: 0.7318 (t) REVERT: k 120 VAL cc_start: 0.7903 (m) cc_final: 0.7589 (p) REVERT: k 121 THR cc_start: 0.8140 (t) cc_final: 0.7925 (p) REVERT: l 9 PHE cc_start: 0.8513 (m-80) cc_final: 0.8249 (m-80) REVERT: l 55 ARG cc_start: 0.7383 (ttm110) cc_final: 0.6974 (ttp80) REVERT: m 44 LEU cc_start: 0.8236 (tp) cc_final: 0.7917 (tp) REVERT: o 29 LYS cc_start: 0.8642 (mttm) cc_final: 0.8294 (mtpt) REVERT: o 34 GLU cc_start: 0.7416 (pp20) cc_final: 0.7081 (pt0) REVERT: o 60 THR cc_start: 0.9186 (m) cc_final: 0.8122 (m) REVERT: p 11 ARG cc_start: 0.7529 (tpm170) cc_final: 0.7272 (tpp80) REVERT: q 23 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7684 (mm-30) REVERT: r 19 LEU cc_start: 0.7822 (mt) cc_final: 0.7618 (mp) REVERT: s 80 TRP cc_start: 0.8351 (p-90) cc_final: 0.7992 (p-90) REVERT: t 87 PHE cc_start: 0.7347 (m-80) cc_final: 0.6832 (m-10) REVERT: t 100 SER cc_start: 0.7580 (m) cc_final: 0.7260 (t) REVERT: v 68 LYS cc_start: 0.7241 (tptp) cc_final: 0.6487 (ttmt) REVERT: v 70 GLU cc_start: 0.7439 (pm20) cc_final: 0.6941 (pm20) REVERT: w 62 LYS cc_start: 0.8320 (mttt) cc_final: 0.8094 (mtpp) REVERT: x 31 GLN cc_start: 0.6962 (mt0) cc_final: 0.6652 (tt0) REVERT: z 12 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7633 (mmmt) REVERT: 0 7 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6900 (mm-30) REVERT: 0 10 LYS cc_start: 0.7112 (ptpt) cc_final: 0.6904 (pttt) REVERT: 0 50 LYS cc_start: 0.7939 (ptpt) cc_final: 0.6745 (mmtm) REVERT: 2 29 LEU cc_start: 0.8576 (mt) cc_final: 0.8229 (tt) REVERT: 3 1 MET cc_start: 0.7361 (tpp) cc_final: 0.6963 (tpp) outliers start: 102 outliers final: 30 residues processed: 1580 average time/residue: 1.5150 time to fit residues: 3968.7499 Evaluate side-chains 968 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 929 time to evaluate : 7.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain U residue 33 ARG Chi-restraints excluded: chain U residue 35 ARG Chi-restraints excluded: chain U residue 44 GLU Chi-restraints excluded: chain U residue 47 ARG Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 63 GLU Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 62 ILE Chi-restraints excluded: chain Y residue 68 VAL Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 79 PHE Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 109 THR Chi-restraints excluded: chain Y residue 117 LYS Chi-restraints excluded: chain Y residue 120 PHE Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 144 THR Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Y residue 154 PHE Chi-restraints excluded: chain Y residue 163 ARG Chi-restraints excluded: chain Y residue 173 VAL Chi-restraints excluded: chain e residue 176 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 871 optimal weight: 0.0040 chunk 782 optimal weight: 0.9980 chunk 434 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 527 optimal weight: 6.9990 chunk 417 optimal weight: 6.9990 chunk 808 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 chunk 491 optimal weight: 4.9990 chunk 602 optimal weight: 10.0000 chunk 937 optimal weight: 3.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS D 59 GLN E 148 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN K 40 ASN K 119 ASN O 35 GLN P 26 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN T 21 ASN U 56 HIS ** Y 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN d 36 GLN d 49 GLN f 52 ASN g 73 ASN h 73 ASN ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN k 104 GLN l 60 GLN m 18 GLN p 20 GLN s 48 GLN s 91 GLN u 49 ASN u 75 GLN x 58 ASN 2 31 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 160094 Z= 0.297 Angle : 0.724 15.497 239525 Z= 0.384 Chirality : 0.039 0.419 30521 Planarity : 0.007 0.134 12814 Dihedral : 23.792 179.063 80211 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.06 % Favored : 94.75 % Rotamer: Outliers : 3.41 % Allowed : 12.20 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.11), residues: 5767 helix: 0.67 (0.12), residues: 1903 sheet: -0.56 (0.16), residues: 1077 loop : -1.14 (0.12), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 23 HIS 0.023 0.002 HIS l 13 PHE 0.023 0.002 PHE h 91 TYR 0.019 0.002 TYR f 128 ARG 0.007 0.001 ARG Y 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 990 time to evaluate : 6.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 TRP cc_start: 0.7470 (p-90) cc_final: 0.7234 (p-90) REVERT: B 45 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.5721 (tptt) REVERT: C 21 THR cc_start: 0.8466 (p) cc_final: 0.7220 (p) REVERT: C 144 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6692 (mm) REVERT: C 154 SER cc_start: 0.8847 (t) cc_final: 0.8514 (p) REVERT: C 162 ILE cc_start: 0.8649 (mt) cc_final: 0.8196 (pt) REVERT: C 183 ASP cc_start: 0.8570 (t0) cc_final: 0.8249 (t0) REVERT: C 187 SER cc_start: 0.8706 (t) cc_final: 0.8345 (m) REVERT: D 46 PRO cc_start: 0.6468 (Cg_endo) cc_final: 0.6175 (Cg_exo) REVERT: D 69 GLU cc_start: 0.8215 (tp30) cc_final: 0.7438 (tp30) REVERT: D 91 LEU cc_start: 0.7896 (mt) cc_final: 0.7686 (mt) REVERT: E 45 ARG cc_start: 0.7206 (mmm-85) cc_final: 0.6871 (ttt-90) REVERT: E 66 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8374 (mmmt) REVERT: E 97 GLN cc_start: 0.8425 (tt0) cc_final: 0.7931 (tt0) REVERT: E 146 ASN cc_start: 0.7476 (m-40) cc_final: 0.7190 (m110) REVERT: E 147 MET cc_start: 0.8010 (ttp) cc_final: 0.7649 (ttp) REVERT: F 9 MET cc_start: 0.7615 (ptm) cc_final: 0.7256 (ptt) REVERT: G 74 GLU cc_start: 0.7743 (pt0) cc_final: 0.7499 (pt0) REVERT: G 139 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7302 (mm-30) REVERT: H 38 ASN cc_start: 0.7589 (m-40) cc_final: 0.6701 (m110) REVERT: H 50 LYS cc_start: 0.7325 (ptmt) cc_final: 0.7088 (ptmm) REVERT: I 37 GLN cc_start: 0.6915 (pp30) cc_final: 0.6504 (pm20) REVERT: I 46 MET cc_start: 0.7370 (tpp) cc_final: 0.7092 (tpp) REVERT: I 112 GLU cc_start: 0.7664 (tt0) cc_final: 0.7104 (tt0) REVERT: J 14 ASP cc_start: 0.6629 (t0) cc_final: 0.6257 (t0) REVERT: J 97 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: K 18 ASP cc_start: 0.6940 (m-30) cc_final: 0.6574 (p0) REVERT: K 85 MET cc_start: 0.7852 (mtt) cc_final: 0.7494 (mtt) REVERT: K 86 VAL cc_start: 0.8115 (t) cc_final: 0.7634 (p) REVERT: L 115 SER cc_start: 0.8882 (p) cc_final: 0.8644 (p) REVERT: O 85 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7285 (mt) REVERT: P 76 LYS cc_start: 0.8134 (ttmm) cc_final: 0.7589 (ttpt) REVERT: Q 62 ARG cc_start: 0.7864 (tmm-80) cc_final: 0.7636 (tmm-80) REVERT: R 16 GLU cc_start: 0.2825 (OUTLIER) cc_final: 0.2531 (tp30) REVERT: R 61 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8296 (mtm180) REVERT: S 71 LEU cc_start: 0.9085 (mp) cc_final: 0.8811 (mt) REVERT: T 39 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7924 (mp) REVERT: T 70 ASN cc_start: 0.8052 (m-40) cc_final: 0.7404 (m110) REVERT: U 4 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7607 (pt) REVERT: U 33 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7584 (mtt-85) REVERT: Y 33 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7782 (mttt) REVERT: Y 116 VAL cc_start: 0.7043 (OUTLIER) cc_final: 0.6632 (m) REVERT: Y 117 LYS cc_start: 0.5093 (OUTLIER) cc_final: 0.4824 (mtmm) REVERT: Y 154 PHE cc_start: 0.5451 (OUTLIER) cc_final: 0.4938 (p90) REVERT: c 28 LYS cc_start: 0.8353 (mmtm) cc_final: 0.8121 (mmtp) REVERT: c 116 ILE cc_start: 0.8909 (pt) cc_final: 0.8510 (mt) REVERT: c 264 ASP cc_start: 0.8188 (m-30) cc_final: 0.7818 (m-30) REVERT: e 115 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7554 (mt0) REVERT: e 176 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6968 (t70) REVERT: e 184 ASP cc_start: 0.7448 (t0) cc_final: 0.6423 (m-30) REVERT: e 191 ASP cc_start: 0.7030 (t0) cc_final: 0.6726 (t0) REVERT: f 61 SER cc_start: 0.7689 (m) cc_final: 0.7332 (p) REVERT: f 78 LYS cc_start: 0.7508 (mtmt) cc_final: 0.7169 (ptpt) REVERT: f 134 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7716 (tp30) REVERT: i 16 TYR cc_start: 0.8122 (m-80) cc_final: 0.7737 (m-80) REVERT: j 56 ASP cc_start: 0.7392 (m-30) cc_final: 0.7103 (m-30) REVERT: j 82 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8458 (m-40) REVERT: j 97 THR cc_start: 0.7898 (p) cc_final: 0.7549 (t) REVERT: j 104 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.9037 (m) REVERT: l 55 ARG cc_start: 0.7477 (ttm110) cc_final: 0.7122 (ttp80) REVERT: p 11 ARG cc_start: 0.7728 (tpm170) cc_final: 0.7422 (tpp80) REVERT: q 2 TYR cc_start: 0.8126 (p90) cc_final: 0.7899 (p90) REVERT: q 23 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7751 (mm-30) REVERT: r 85 ILE cc_start: 0.8874 (mm) cc_final: 0.8536 (tt) REVERT: s 92 ASN cc_start: 0.6060 (p0) cc_final: 0.5758 (p0) REVERT: t 22 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7958 (mtp-110) REVERT: t 86 ARG cc_start: 0.7679 (mtm110) cc_final: 0.7409 (ttp-110) REVERT: t 87 PHE cc_start: 0.7346 (m-80) cc_final: 0.6931 (m-10) REVERT: v 68 LYS cc_start: 0.7377 (tptp) cc_final: 0.6757 (ttmt) REVERT: v 70 GLU cc_start: 0.7446 (pm20) cc_final: 0.7038 (pm20) REVERT: w 62 LYS cc_start: 0.8360 (mttt) cc_final: 0.8070 (mtpp) REVERT: x 30 MET cc_start: 0.8433 (mmm) cc_final: 0.8217 (mmm) REVERT: z 12 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7851 (mmmt) REVERT: 0 7 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6852 (mm-30) REVERT: 0 10 LYS cc_start: 0.7076 (ptpt) cc_final: 0.6776 (pttt) REVERT: 0 50 LYS cc_start: 0.8182 (ptpt) cc_final: 0.6998 (mmtt) REVERT: 2 29 LEU cc_start: 0.8665 (mt) cc_final: 0.8283 (tt) REVERT: 2 55 LEU cc_start: 0.8225 (tp) cc_final: 0.7928 (tp) REVERT: 2 62 LEU cc_start: 0.8215 (tt) cc_final: 0.7961 (tt) REVERT: 3 1 MET cc_start: 0.7505 (tpp) cc_final: 0.6894 (tpp) REVERT: 4 63 ARG cc_start: 0.6356 (ptm160) cc_final: 0.6101 (ptm160) outliers start: 164 outliers final: 88 residues processed: 1089 average time/residue: 1.3946 time to fit residues: 2607.3818 Evaluate side-chains 988 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 885 time to evaluate : 6.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 23 CYS Chi-restraints excluded: chain U residue 33 ARG Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 33 LYS Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 81 GLU Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 102 TYR Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain Y residue 117 LYS Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Y residue 154 PHE Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 176 ASP Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 19 ILE Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain h residue 73 ASN Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 187 THR Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain m residue 97 ILE Chi-restraints excluded: chain n residue 89 ASP Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 75 SER Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 77 THR Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 51 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain z residue 22 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 520 optimal weight: 20.0000 chunk 290 optimal weight: 6.9990 chunk 779 optimal weight: 1.9990 chunk 638 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 chunk 938 optimal weight: 9.9990 chunk 1014 optimal weight: 5.9990 chunk 836 optimal weight: 1.9990 chunk 931 optimal weight: 2.9990 chunk 320 optimal weight: 9.9990 chunk 753 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN G 9 GLN G 130 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN K 119 ASN P 26 ASN P 29 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN Y 125 ASN ** Y 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN f 52 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN ** m 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 20 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 160094 Z= 0.209 Angle : 0.624 14.159 239525 Z= 0.341 Chirality : 0.035 0.405 30521 Planarity : 0.006 0.131 12814 Dihedral : 23.674 179.204 80169 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.50 % Favored : 94.36 % Rotamer: Outliers : 3.79 % Allowed : 15.19 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.11), residues: 5767 helix: 1.04 (0.12), residues: 1902 sheet: -0.41 (0.16), residues: 1054 loop : -1.06 (0.11), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 23 HIS 0.014 0.001 HIS l 13 PHE 0.016 0.002 PHE v 69 TYR 0.019 0.002 TYR D 103 ARG 0.011 0.001 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 950 time to evaluate : 6.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.5422 (tptt) REVERT: B 118 GLU cc_start: 0.5767 (pp20) cc_final: 0.5535 (tm-30) REVERT: B 161 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8492 (tt) REVERT: C 21 THR cc_start: 0.8109 (p) cc_final: 0.7738 (p) REVERT: C 144 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6634 (mm) REVERT: C 154 SER cc_start: 0.8802 (t) cc_final: 0.8503 (p) REVERT: C 183 ASP cc_start: 0.8541 (t0) cc_final: 0.8029 (t0) REVERT: C 187 SER cc_start: 0.8695 (t) cc_final: 0.8356 (m) REVERT: D 46 PRO cc_start: 0.6630 (Cg_endo) cc_final: 0.6324 (Cg_exo) REVERT: D 58 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6874 (tttm) REVERT: D 69 GLU cc_start: 0.8200 (tp30) cc_final: 0.7511 (tp30) REVERT: D 91 LEU cc_start: 0.7820 (mt) cc_final: 0.7560 (mt) REVERT: D 103 TYR cc_start: 0.7882 (t80) cc_final: 0.7562 (t80) REVERT: D 154 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.5969 (mtm180) REVERT: E 45 ARG cc_start: 0.7293 (mmm-85) cc_final: 0.7010 (ttp-110) REVERT: E 48 PHE cc_start: 0.8793 (p90) cc_final: 0.8466 (p90) REVERT: E 66 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8357 (mmmt) REVERT: E 78 ASN cc_start: 0.7113 (t0) cc_final: 0.6810 (t0) REVERT: E 97 GLN cc_start: 0.8456 (tt0) cc_final: 0.7986 (tt0) REVERT: E 146 ASN cc_start: 0.7478 (m-40) cc_final: 0.7143 (m110) REVERT: F 9 MET cc_start: 0.7634 (ptm) cc_final: 0.7287 (ptt) REVERT: F 42 TRP cc_start: 0.7010 (m-10) cc_final: 0.6736 (m-10) REVERT: G 139 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7339 (mm-30) REVERT: H 27 MET cc_start: 0.7090 (ptp) cc_final: 0.6795 (ptp) REVERT: H 38 ASN cc_start: 0.7520 (m-40) cc_final: 0.6588 (m110) REVERT: H 50 LYS cc_start: 0.7236 (ptmt) cc_final: 0.6990 (ptmm) REVERT: I 37 GLN cc_start: 0.7026 (pp30) cc_final: 0.6361 (pm20) REVERT: I 46 MET cc_start: 0.7329 (tpp) cc_final: 0.7034 (tpp) REVERT: I 112 GLU cc_start: 0.7849 (tt0) cc_final: 0.7350 (tt0) REVERT: J 14 ASP cc_start: 0.6679 (t0) cc_final: 0.6292 (t0) REVERT: J 37 ARG cc_start: 0.7176 (mtp85) cc_final: 0.6957 (mtt90) REVERT: K 18 ASP cc_start: 0.7110 (m-30) cc_final: 0.6591 (p0) REVERT: K 85 MET cc_start: 0.7441 (mtt) cc_final: 0.7075 (mtt) REVERT: K 86 VAL cc_start: 0.7995 (t) cc_final: 0.7445 (p) REVERT: L 115 SER cc_start: 0.8845 (p) cc_final: 0.8618 (p) REVERT: O 85 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7144 (mt) REVERT: P 76 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7373 (pttt) REVERT: Q 28 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7787 (t80) REVERT: R 16 GLU cc_start: 0.2606 (OUTLIER) cc_final: 0.2098 (tp30) REVERT: R 61 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.8154 (ttm110) REVERT: S 71 LEU cc_start: 0.9131 (mp) cc_final: 0.8896 (mt) REVERT: T 39 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7899 (mp) REVERT: T 70 ASN cc_start: 0.8031 (m-40) cc_final: 0.7508 (m110) REVERT: U 4 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7519 (pt) REVERT: U 33 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7469 (mtt-85) REVERT: Y 33 LYS cc_start: 0.8001 (mttp) cc_final: 0.7757 (mttt) REVERT: Y 117 LYS cc_start: 0.5214 (OUTLIER) cc_final: 0.4940 (mtmm) REVERT: c 4 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8817 (m) REVERT: c 116 ILE cc_start: 0.8867 (pt) cc_final: 0.8548 (mt) REVERT: c 120 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7558 (m) REVERT: c 264 ASP cc_start: 0.8214 (m-30) cc_final: 0.7866 (m-30) REVERT: e 115 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7491 (mt0) REVERT: e 176 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6434 (m-30) REVERT: e 184 ASP cc_start: 0.7406 (t0) cc_final: 0.6360 (m-30) REVERT: f 42 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6699 (pm20) REVERT: f 61 SER cc_start: 0.7718 (m) cc_final: 0.7497 (p) REVERT: f 78 LYS cc_start: 0.7518 (mtmt) cc_final: 0.7157 (ptpt) REVERT: g 114 ASP cc_start: 0.8309 (t0) cc_final: 0.7679 (m-30) REVERT: h 91 PHE cc_start: 0.1012 (OUTLIER) cc_final: 0.0151 (t80) REVERT: i 16 TYR cc_start: 0.8050 (m-80) cc_final: 0.7686 (m-80) REVERT: j 56 ASP cc_start: 0.7429 (m-30) cc_final: 0.7181 (m-30) REVERT: j 104 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9071 (m) REVERT: p 11 ARG cc_start: 0.7787 (tpm170) cc_final: 0.7448 (tpp80) REVERT: q 23 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7750 (mm-30) REVERT: r 85 ILE cc_start: 0.8829 (mm) cc_final: 0.8580 (tt) REVERT: s 92 ASN cc_start: 0.5892 (p0) cc_final: 0.5597 (p0) REVERT: t 22 ARG cc_start: 0.8226 (tpp80) cc_final: 0.8011 (mtp-110) REVERT: t 67 VAL cc_start: 0.9037 (p) cc_final: 0.8817 (t) REVERT: t 86 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7435 (ttp-110) REVERT: t 87 PHE cc_start: 0.7272 (m-80) cc_final: 0.6956 (m-10) REVERT: u 10 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7850 (pttm) REVERT: v 25 ARG cc_start: 0.7769 (mmt-90) cc_final: 0.7468 (mmp80) REVERT: v 68 LYS cc_start: 0.7304 (tptp) cc_final: 0.6668 (ttmt) REVERT: v 70 GLU cc_start: 0.7420 (pm20) cc_final: 0.6979 (pm20) REVERT: w 62 LYS cc_start: 0.8352 (mttt) cc_final: 0.8130 (mtpp) REVERT: x 30 MET cc_start: 0.8284 (mmm) cc_final: 0.8077 (mmm) REVERT: z 12 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7747 (mmmt) REVERT: 2 55 LEU cc_start: 0.8169 (tp) cc_final: 0.7874 (tp) outliers start: 182 outliers final: 110 residues processed: 1061 average time/residue: 1.4153 time to fit residues: 2590.7040 Evaluate side-chains 1002 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 874 time to evaluate : 6.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 23 CYS Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 33 ARG Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 102 TYR Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 109 THR Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 117 LYS Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain c residue 4 VAL Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 176 ASP Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 104 THR Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 2 LEU Chi-restraints excluded: chain l residue 26 VAL Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 181 ILE Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 97 ILE Chi-restraints excluded: chain o residue 104 THR Chi-restraints excluded: chain p residue 75 SER Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 77 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain y residue 5 ILE Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain 0 residue 48 ILE Chi-restraints excluded: chain 3 residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 927 optimal weight: 0.9980 chunk 705 optimal weight: 10.0000 chunk 487 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 448 optimal weight: 10.0000 chunk 630 optimal weight: 30.0000 chunk 942 optimal weight: 2.9990 chunk 997 optimal weight: 1.9990 chunk 492 optimal weight: 7.9990 chunk 892 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS C 6 HIS G 9 GLN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN P 29 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN Y 125 ASN c 239 ASN d 36 GLN f 52 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 2 GLN h 66 ASN ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 135 HIS i 80 HIS m 62 ASN p 20 GLN p 59 GLN s 70 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 160094 Z= 0.310 Angle : 0.701 14.916 239525 Z= 0.374 Chirality : 0.039 0.381 30521 Planarity : 0.007 0.132 12814 Dihedral : 23.621 178.603 80159 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer: Outliers : 4.83 % Allowed : 17.25 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.11), residues: 5767 helix: 0.81 (0.12), residues: 1897 sheet: -0.59 (0.15), residues: 1073 loop : -1.16 (0.11), residues: 2797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 23 HIS 0.014 0.001 HIS l 13 PHE 0.028 0.002 PHE Y 79 TYR 0.019 0.002 TYR 0 49 ARG 0.009 0.001 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 924 time to evaluate : 6.596 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: B 118 GLU cc_start: 0.5865 (pp20) cc_final: 0.5549 (tm-30) REVERT: B 161 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8556 (tt) REVERT: C 21 THR cc_start: 0.8044 (p) cc_final: 0.7651 (p) REVERT: C 144 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6647 (mm) REVERT: C 154 SER cc_start: 0.8904 (t) cc_final: 0.8537 (p) REVERT: C 183 ASP cc_start: 0.8586 (t0) cc_final: 0.7993 (t70) REVERT: C 187 SER cc_start: 0.8717 (t) cc_final: 0.8367 (m) REVERT: C 192 THR cc_start: 0.8137 (m) cc_final: 0.7815 (p) REVERT: D 46 PRO cc_start: 0.6604 (Cg_endo) cc_final: 0.6295 (Cg_exo) REVERT: D 58 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7066 (tttm) REVERT: D 69 GLU cc_start: 0.8410 (tp30) cc_final: 0.8124 (tp30) REVERT: D 91 LEU cc_start: 0.7738 (mt) cc_final: 0.7421 (mt) REVERT: D 154 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.6044 (mtm180) REVERT: E 45 ARG cc_start: 0.7233 (mmm-85) cc_final: 0.6923 (ttp-110) REVERT: E 48 PHE cc_start: 0.8829 (p90) cc_final: 0.8578 (p90) REVERT: E 66 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8457 (mmmt) REVERT: E 97 GLN cc_start: 0.8441 (tt0) cc_final: 0.7997 (tt0) REVERT: E 146 ASN cc_start: 0.7570 (m-40) cc_final: 0.6888 (m-40) REVERT: E 147 MET cc_start: 0.7772 (ttp) cc_final: 0.7319 (ttp) REVERT: G 90 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6256 (mm-30) REVERT: G 129 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6981 (pm20) REVERT: G 139 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7341 (mm-30) REVERT: H 38 ASN cc_start: 0.7437 (m-40) cc_final: 0.6624 (m110) REVERT: I 18 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6147 (mtp180) REVERT: I 37 GLN cc_start: 0.7051 (pp30) cc_final: 0.6453 (pm20) REVERT: I 46 MET cc_start: 0.7342 (tpp) cc_final: 0.7049 (tpp) REVERT: I 112 GLU cc_start: 0.7988 (tt0) cc_final: 0.7612 (tt0) REVERT: J 14 ASP cc_start: 0.6734 (t0) cc_final: 0.6482 (t0) REVERT: J 37 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6809 (mtp85) REVERT: K 18 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6279 (p0) REVERT: K 85 MET cc_start: 0.7520 (mtt) cc_final: 0.7206 (mtt) REVERT: K 86 VAL cc_start: 0.7953 (t) cc_final: 0.7536 (p) REVERT: L 15 LYS cc_start: 0.7044 (mmtm) cc_final: 0.6556 (mmmt) REVERT: L 43 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7356 (mtpp) REVERT: L 115 SER cc_start: 0.8869 (p) cc_final: 0.8647 (p) REVERT: O 17 ARG cc_start: 0.5303 (mpp-170) cc_final: 0.5022 (ptp-170) REVERT: O 85 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7168 (mm) REVERT: P 66 THR cc_start: 0.8350 (t) cc_final: 0.8062 (p) REVERT: P 76 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7449 (pttt) REVERT: R 61 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.7602 (mtt90) REVERT: S 71 LEU cc_start: 0.9198 (mp) cc_final: 0.8712 (mp) REVERT: T 39 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7846 (mp) REVERT: T 70 ASN cc_start: 0.8065 (m-40) cc_final: 0.7474 (m110) REVERT: Y 117 LYS cc_start: 0.5330 (OUTLIER) cc_final: 0.5115 (mtmm) REVERT: Y 124 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6381 (tp) REVERT: c 98 ASP cc_start: 0.7939 (p0) cc_final: 0.7729 (p0) REVERT: c 116 ILE cc_start: 0.8935 (pt) cc_final: 0.8656 (mt) REVERT: c 180 GLU cc_start: 0.7639 (tt0) cc_final: 0.7113 (tt0) REVERT: c 194 GLU cc_start: 0.8402 (mp0) cc_final: 0.8190 (mt-10) REVERT: c 214 ARG cc_start: 0.8701 (mtm180) cc_final: 0.8310 (mtt90) REVERT: c 264 ASP cc_start: 0.8206 (m-30) cc_final: 0.7960 (m-30) REVERT: e 115 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7438 (mt0) REVERT: e 145 ASP cc_start: 0.5830 (OUTLIER) cc_final: 0.5066 (m-30) REVERT: e 184 ASP cc_start: 0.7388 (t0) cc_final: 0.6264 (m-30) REVERT: e 191 ASP cc_start: 0.7153 (t0) cc_final: 0.6892 (t0) REVERT: f 78 LYS cc_start: 0.7609 (mtmt) cc_final: 0.7271 (ptpt) REVERT: f 142 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6537 (m-30) REVERT: g 42 GLU cc_start: 0.6173 (tp30) cc_final: 0.5916 (tp30) REVERT: g 117 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7746 (mm) REVERT: g 130 GLU cc_start: 0.8015 (tt0) cc_final: 0.7749 (tt0) REVERT: g 153 ARG cc_start: 0.7111 (mtp85) cc_final: 0.6889 (mtp85) REVERT: h 91 PHE cc_start: 0.1305 (OUTLIER) cc_final: 0.0484 (t80) REVERT: i 88 THR cc_start: 0.8829 (p) cc_final: 0.8526 (t) REVERT: j 56 ASP cc_start: 0.7496 (m-30) cc_final: 0.7227 (m-30) REVERT: j 82 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8526 (m-40) REVERT: k 143 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7069 (tm-30) REVERT: n 80 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6833 (pt0) REVERT: o 89 ARG cc_start: 0.6956 (mtm110) cc_final: 0.6597 (mtm110) REVERT: p 11 ARG cc_start: 0.7836 (tpm170) cc_final: 0.7450 (tpp80) REVERT: q 23 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7791 (mm-30) REVERT: r 85 ILE cc_start: 0.8831 (mm) cc_final: 0.8626 (tt) REVERT: r 95 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.7935 (ttt180) REVERT: s 21 SER cc_start: 0.7995 (m) cc_final: 0.7693 (p) REVERT: s 92 ASN cc_start: 0.6079 (p0) cc_final: 0.5721 (p0) REVERT: t 9 ASP cc_start: 0.7822 (m-30) cc_final: 0.7063 (t0) REVERT: t 86 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7446 (ttp-110) REVERT: t 87 PHE cc_start: 0.7251 (m-80) cc_final: 0.6898 (m-10) REVERT: u 10 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7868 (pttm) REVERT: u 57 TYR cc_start: 0.8323 (m-80) cc_final: 0.8049 (m-80) REVERT: v 25 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7519 (mmp80) REVERT: v 68 LYS cc_start: 0.7381 (tptp) cc_final: 0.6574 (ttpt) REVERT: v 70 GLU cc_start: 0.7525 (pm20) cc_final: 0.6881 (pm20) REVERT: x 30 MET cc_start: 0.8349 (mmm) cc_final: 0.8098 (mmm) REVERT: z 12 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7865 (mmmt) REVERT: 0 37 LYS cc_start: 0.7376 (mmmm) cc_final: 0.7167 (ttmt) outliers start: 232 outliers final: 154 residues processed: 1072 average time/residue: 1.3911 time to fit residues: 2570.5765 Evaluate side-chains 1046 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 875 time to evaluate : 6.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 15 HIS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 90 GLU Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 22 LYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 18 ASP Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain S residue 4 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 117 LYS Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Y residue 128 ARG Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 51 THR Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 199 GLU Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain h residue 19 VAL Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 40 THR Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain i residue 5 THR Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain l residue 181 ILE Chi-restraints excluded: chain l residue 187 THR Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain m residue 97 ILE Chi-restraints excluded: chain n residue 89 ASP Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 75 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 77 THR Chi-restraints excluded: chain u residue 60 VAL Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 51 VAL Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain y residue 55 VAL Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 33 THR Chi-restraints excluded: chain z residue 40 ARG Chi-restraints excluded: chain 3 residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 830 optimal weight: 7.9990 chunk 566 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 742 optimal weight: 0.8980 chunk 411 optimal weight: 0.0270 chunk 851 optimal weight: 1.9990 chunk 689 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 509 optimal weight: 7.9990 chunk 895 optimal weight: 0.2980 chunk 251 optimal weight: 0.0770 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 ASN I 37 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 161 GLN f 52 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 ASN h 73 ASN ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN p 20 GLN s 70 HIS ** z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.138 160094 Z= 0.125 Angle : 0.582 13.799 239525 Z= 0.321 Chirality : 0.033 0.391 30521 Planarity : 0.006 0.122 12814 Dihedral : 23.583 179.022 80144 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 2.64 % Allowed : 20.25 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 5767 helix: 1.23 (0.12), residues: 1919 sheet: -0.32 (0.16), residues: 1069 loop : -0.95 (0.12), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 95 HIS 0.008 0.001 HIS l 13 PHE 0.021 0.001 PHE t 73 TYR 0.018 0.001 TYR D 103 ARG 0.009 0.000 ARG j 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 960 time to evaluate : 6.565 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: B 118 GLU cc_start: 0.5775 (pp20) cc_final: 0.5497 (tm-30) REVERT: B 161 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8470 (tt) REVERT: C 21 THR cc_start: 0.8175 (p) cc_final: 0.7821 (p) REVERT: C 114 LYS cc_start: 0.8035 (tptt) cc_final: 0.7828 (tptp) REVERT: C 144 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6666 (mm) REVERT: C 154 SER cc_start: 0.8887 (t) cc_final: 0.8583 (p) REVERT: C 183 ASP cc_start: 0.8498 (t0) cc_final: 0.7884 (t70) REVERT: C 184 TYR cc_start: 0.8893 (t80) cc_final: 0.8688 (t80) REVERT: C 187 SER cc_start: 0.8723 (t) cc_final: 0.8335 (m) REVERT: C 192 THR cc_start: 0.8003 (m) cc_final: 0.7687 (p) REVERT: D 46 PRO cc_start: 0.6622 (Cg_endo) cc_final: 0.6299 (Cg_exo) REVERT: D 58 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6764 (tttm) REVERT: D 69 GLU cc_start: 0.8248 (tp30) cc_final: 0.7518 (tp30) REVERT: D 91 LEU cc_start: 0.7736 (mt) cc_final: 0.7435 (mt) REVERT: D 135 TYR cc_start: 0.7422 (t80) cc_final: 0.6953 (t80) REVERT: D 154 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6188 (mtm180) REVERT: E 20 ARG cc_start: 0.7366 (ttt180) cc_final: 0.7054 (ttt90) REVERT: E 66 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8382 (mmmt) REVERT: E 78 ASN cc_start: 0.7537 (t0) cc_final: 0.6873 (p0) REVERT: E 97 GLN cc_start: 0.8410 (tt0) cc_final: 0.7966 (tt0) REVERT: E 146 ASN cc_start: 0.7521 (m-40) cc_final: 0.6708 (m-40) REVERT: F 2 ARG cc_start: 0.7521 (mtp85) cc_final: 0.7261 (mtp180) REVERT: F 17 GLN cc_start: 0.6360 (mt0) cc_final: 0.5946 (tt0) REVERT: F 33 GLU cc_start: 0.6932 (tp30) cc_final: 0.6728 (tp30) REVERT: F 44 ARG cc_start: 0.7080 (mtp-110) cc_final: 0.6814 (mtp85) REVERT: H 27 MET cc_start: 0.7113 (ptp) cc_final: 0.6884 (ptp) REVERT: I 37 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6387 (pm20) REVERT: I 46 MET cc_start: 0.7242 (tpp) cc_final: 0.6956 (tpp) REVERT: I 112 GLU cc_start: 0.7918 (tt0) cc_final: 0.7473 (tt0) REVERT: J 37 ARG cc_start: 0.7067 (mtp85) cc_final: 0.6863 (mtp85) REVERT: K 85 MET cc_start: 0.7169 (mtt) cc_final: 0.6897 (mtt) REVERT: L 15 LYS cc_start: 0.6982 (mmtm) cc_final: 0.6555 (mmmt) REVERT: L 43 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7440 (mtpp) REVERT: L 78 SER cc_start: 0.8456 (m) cc_final: 0.8000 (m) REVERT: L 115 SER cc_start: 0.8785 (p) cc_final: 0.8569 (p) REVERT: O 17 ARG cc_start: 0.5340 (mpp-170) cc_final: 0.5065 (ptp-170) REVERT: O 85 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7249 (mm) REVERT: P 66 THR cc_start: 0.8361 (t) cc_final: 0.8074 (p) REVERT: P 76 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7482 (pttt) REVERT: Q 28 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7762 (t80) REVERT: R 43 ARG cc_start: 0.8236 (ptp90) cc_final: 0.8031 (ptp90) REVERT: S 71 LEU cc_start: 0.9167 (mp) cc_final: 0.8956 (mt) REVERT: T 70 ASN cc_start: 0.7967 (m-40) cc_final: 0.7421 (m110) REVERT: U 4 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7194 (mm) REVERT: U 33 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7312 (mtt-85) REVERT: Y 33 LYS cc_start: 0.8096 (mttp) cc_final: 0.7795 (mttt) REVERT: c 98 ASP cc_start: 0.7993 (p0) cc_final: 0.7744 (p0) REVERT: c 132 MET cc_start: 0.7461 (mtm) cc_final: 0.7161 (mtm) REVERT: c 214 ARG cc_start: 0.8538 (mtm180) cc_final: 0.8244 (mtt90) REVERT: c 264 ASP cc_start: 0.8284 (m-30) cc_final: 0.7904 (m-30) REVERT: e 22 ASP cc_start: 0.7609 (p0) cc_final: 0.7089 (m-30) REVERT: e 115 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7526 (mt0) REVERT: e 145 ASP cc_start: 0.5741 (OUTLIER) cc_final: 0.5063 (m-30) REVERT: e 184 ASP cc_start: 0.7320 (t0) cc_final: 0.6208 (m-30) REVERT: e 191 ASP cc_start: 0.7057 (t0) cc_final: 0.6778 (t0) REVERT: f 78 LYS cc_start: 0.7636 (mtmt) cc_final: 0.7375 (ptpt) REVERT: f 142 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: g 42 GLU cc_start: 0.6342 (tp30) cc_final: 0.6094 (tp30) REVERT: g 114 ASP cc_start: 0.8249 (t0) cc_final: 0.7984 (m-30) REVERT: g 117 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7666 (mm) REVERT: g 153 ARG cc_start: 0.7024 (mtp85) cc_final: 0.6766 (ttm170) REVERT: h 91 PHE cc_start: 0.1368 (OUTLIER) cc_final: 0.0487 (t80) REVERT: i 136 GLN cc_start: 0.8203 (mt0) cc_final: 0.7770 (mt0) REVERT: j 56 ASP cc_start: 0.7473 (m-30) cc_final: 0.7231 (m-30) REVERT: j 82 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8373 (m-40) REVERT: j 106 GLU cc_start: 0.7015 (mp0) cc_final: 0.6671 (mp0) REVERT: k 143 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7047 (tm-30) REVERT: n 80 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7049 (pt0) REVERT: o 24 ASP cc_start: 0.8820 (m-30) cc_final: 0.8583 (m-30) REVERT: o 112 GLU cc_start: 0.8041 (tp30) cc_final: 0.7660 (tp30) REVERT: p 11 ARG cc_start: 0.7740 (tpm170) cc_final: 0.7369 (tpp80) REVERT: q 23 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7617 (mm-30) REVERT: r 95 ARG cc_start: 0.8463 (ttp-170) cc_final: 0.7874 (ttt180) REVERT: s 21 SER cc_start: 0.8111 (m) cc_final: 0.7763 (p) REVERT: s 92 ASN cc_start: 0.5954 (p0) cc_final: 0.5547 (p0) REVERT: t 67 VAL cc_start: 0.8998 (p) cc_final: 0.8672 (t) REVERT: t 86 ARG cc_start: 0.7639 (mtm110) cc_final: 0.7156 (ttm-80) REVERT: t 87 PHE cc_start: 0.7144 (m-80) cc_final: 0.6829 (m-10) REVERT: u 10 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7839 (pttm) REVERT: u 57 TYR cc_start: 0.8250 (m-80) cc_final: 0.8037 (m-80) REVERT: v 68 LYS cc_start: 0.7227 (tptp) cc_final: 0.6618 (ttmt) REVERT: v 70 GLU cc_start: 0.7525 (pm20) cc_final: 0.7124 (pm20) REVERT: w 62 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8092 (mtpp) REVERT: x 24 GLU cc_start: 0.8085 (tp30) cc_final: 0.7723 (tt0) REVERT: z 12 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7813 (mmmt) REVERT: 2 55 LEU cc_start: 0.8238 (tp) cc_final: 0.8012 (tp) outliers start: 127 outliers final: 76 residues processed: 1043 average time/residue: 1.3584 time to fit residues: 2433.4256 Evaluate side-chains 972 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 883 time to evaluate : 6.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain c residue 199 GLU Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain e residue 67 ARG Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 163 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain l residue 187 THR Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 89 ASP Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain p residue 75 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 20 VAL Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 33 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 335 optimal weight: 0.9980 chunk 898 optimal weight: 0.6980 chunk 197 optimal weight: 10.0000 chunk 585 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 998 optimal weight: 7.9990 chunk 828 optimal weight: 4.9990 chunk 462 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 330 optimal weight: 6.9990 chunk 524 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS D 140 ASN E 122 ASN F 63 ASN G 130 ASN ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 86 ASN f 52 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN p 20 GLN x 27 ASN ** z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 160094 Z= 0.277 Angle : 0.659 14.524 239525 Z= 0.353 Chirality : 0.037 0.369 30521 Planarity : 0.006 0.131 12814 Dihedral : 23.515 179.401 80138 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 4.20 % Allowed : 19.83 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 5767 helix: 1.07 (0.12), residues: 1903 sheet: -0.41 (0.16), residues: 1060 loop : -1.06 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 23 HIS 0.010 0.001 HIS l 13 PHE 0.042 0.002 PHE H 49 TYR 0.018 0.002 TYR D 103 ARG 0.009 0.001 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 878 time to evaluate : 6.518 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: B 118 GLU cc_start: 0.5840 (pp20) cc_final: 0.5528 (tm-30) REVERT: B 161 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8538 (tt) REVERT: C 21 THR cc_start: 0.8136 (p) cc_final: 0.7759 (p) REVERT: C 144 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6678 (mm) REVERT: C 154 SER cc_start: 0.8892 (t) cc_final: 0.8555 (p) REVERT: C 183 ASP cc_start: 0.8617 (t0) cc_final: 0.7919 (t70) REVERT: C 187 SER cc_start: 0.8681 (t) cc_final: 0.8353 (m) REVERT: C 192 THR cc_start: 0.8095 (m) cc_final: 0.7754 (p) REVERT: D 46 PRO cc_start: 0.6662 (Cg_endo) cc_final: 0.6318 (Cg_exo) REVERT: D 69 GLU cc_start: 0.8389 (tp30) cc_final: 0.8138 (tp30) REVERT: D 91 LEU cc_start: 0.7744 (mt) cc_final: 0.7407 (mt) REVERT: D 135 TYR cc_start: 0.7458 (t80) cc_final: 0.7000 (t80) REVERT: D 154 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6163 (mtm180) REVERT: E 20 ARG cc_start: 0.7190 (ttt180) cc_final: 0.6750 (ttt90) REVERT: E 48 PHE cc_start: 0.8837 (p90) cc_final: 0.8586 (p90) REVERT: E 66 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8513 (mmmt) REVERT: E 78 ASN cc_start: 0.7630 (t0) cc_final: 0.6958 (p0) REVERT: E 97 GLN cc_start: 0.8406 (tt0) cc_final: 0.7997 (tt0) REVERT: E 146 ASN cc_start: 0.7562 (m-40) cc_final: 0.6826 (m-40) REVERT: E 147 MET cc_start: 0.7818 (ttp) cc_final: 0.7306 (ttp) REVERT: F 2 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7290 (mtp180) REVERT: G 129 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6926 (pm20) REVERT: I 37 GLN cc_start: 0.7042 (pp30) cc_final: 0.6364 (pm20) REVERT: I 46 MET cc_start: 0.7213 (tpp) cc_final: 0.6929 (tpp) REVERT: I 112 GLU cc_start: 0.8076 (tt0) cc_final: 0.7713 (tt0) REVERT: K 85 MET cc_start: 0.7332 (mtt) cc_final: 0.7015 (mtt) REVERT: K 86 VAL cc_start: 0.7910 (t) cc_final: 0.7462 (p) REVERT: L 15 LYS cc_start: 0.6803 (mmtm) cc_final: 0.6423 (mmmt) REVERT: L 43 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7492 (mtpp) REVERT: L 78 SER cc_start: 0.8592 (m) cc_final: 0.8100 (m) REVERT: L 115 SER cc_start: 0.8853 (p) cc_final: 0.8645 (p) REVERT: O 17 ARG cc_start: 0.5431 (mpp-170) cc_final: 0.5069 (ptp-170) REVERT: O 85 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7197 (mm) REVERT: P 66 THR cc_start: 0.8326 (t) cc_final: 0.8037 (p) REVERT: P 76 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7409 (pttt) REVERT: Q 28 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8266 (t80) REVERT: S 71 LEU cc_start: 0.9204 (mp) cc_final: 0.8709 (mp) REVERT: T 70 ASN cc_start: 0.8073 (m-40) cc_final: 0.7501 (m110) REVERT: U 4 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7188 (mm) REVERT: U 33 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7290 (mtt-85) REVERT: Y 161 GLN cc_start: 0.7152 (mp-120) cc_final: 0.6879 (mp10) REVERT: c 98 ASP cc_start: 0.7995 (p0) cc_final: 0.7740 (p0) REVERT: c 264 ASP cc_start: 0.8233 (m-30) cc_final: 0.7842 (m-30) REVERT: e 22 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: e 115 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7440 (mt0) REVERT: e 145 ASP cc_start: 0.5895 (OUTLIER) cc_final: 0.5087 (m-30) REVERT: e 184 ASP cc_start: 0.7374 (t0) cc_final: 0.6207 (m-30) REVERT: e 191 ASP cc_start: 0.7173 (t0) cc_final: 0.6901 (t0) REVERT: f 78 LYS cc_start: 0.7683 (mtmt) cc_final: 0.7377 (ptpt) REVERT: f 142 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6641 (m-30) REVERT: f 161 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7719 (tppp) REVERT: g 42 GLU cc_start: 0.6364 (tp30) cc_final: 0.6059 (tp30) REVERT: g 114 ASP cc_start: 0.8368 (t0) cc_final: 0.7865 (m-30) REVERT: g 117 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7649 (mm) REVERT: g 153 ARG cc_start: 0.7058 (mtp85) cc_final: 0.6813 (ttm170) REVERT: h 91 PHE cc_start: 0.1541 (OUTLIER) cc_final: 0.0539 (t80) REVERT: j 32 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: j 56 ASP cc_start: 0.7568 (m-30) cc_final: 0.7302 (m-30) REVERT: j 82 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8493 (m-40) REVERT: j 106 GLU cc_start: 0.7303 (mp0) cc_final: 0.6829 (mp0) REVERT: k 143 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7066 (tm-30) REVERT: n 80 GLU cc_start: 0.7753 (mt-10) cc_final: 0.6980 (pt0) REVERT: o 112 GLU cc_start: 0.8055 (tp30) cc_final: 0.7623 (tp30) REVERT: p 11 ARG cc_start: 0.7812 (tpm170) cc_final: 0.7407 (tpp80) REVERT: q 23 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7711 (mm-30) REVERT: r 67 ASP cc_start: 0.7166 (t0) cc_final: 0.6418 (p0) REVERT: r 95 ARG cc_start: 0.8509 (ttp-170) cc_final: 0.7875 (ttt180) REVERT: s 21 SER cc_start: 0.8100 (m) cc_final: 0.7792 (p) REVERT: s 92 ASN cc_start: 0.5945 (OUTLIER) cc_final: 0.5541 (p0) REVERT: t 9 ASP cc_start: 0.7838 (m-30) cc_final: 0.7115 (t0) REVERT: t 86 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7379 (ttp-110) REVERT: t 87 PHE cc_start: 0.7173 (m-80) cc_final: 0.6831 (m-10) REVERT: u 10 LYS cc_start: 0.8071 (mmtm) cc_final: 0.7842 (pttm) REVERT: v 68 LYS cc_start: 0.7340 (tptp) cc_final: 0.6920 (tttp) REVERT: v 70 GLU cc_start: 0.7624 (pm20) cc_final: 0.7205 (pm20) REVERT: z 12 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7959 (mmmt) REVERT: z 36 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6517 (mt-10) outliers start: 202 outliers final: 136 residues processed: 1004 average time/residue: 1.3771 time to fit residues: 2390.8625 Evaluate side-chains 998 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 847 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 109 THR Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 199 GLU Chi-restraints excluded: chain d residue 12 THR Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 22 ASP Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain f residue 38 MET Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 26 VAL Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain l residue 181 ILE Chi-restraints excluded: chain l residue 187 THR Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 87 ILE Chi-restraints excluded: chain n residue 89 ASP Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 75 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 92 ASN Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 77 THR Chi-restraints excluded: chain u residue 60 VAL Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 51 VAL Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 33 THR Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 4 residue 13 THR Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 962 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 568 optimal weight: 10.0000 chunk 729 optimal weight: 7.9990 chunk 564 optimal weight: 10.0000 chunk 840 optimal weight: 1.9990 chunk 557 optimal weight: 10.0000 chunk 994 optimal weight: 0.9990 chunk 622 optimal weight: 7.9990 chunk 606 optimal weight: 8.9990 chunk 459 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS D 140 ASN E 73 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 53 HIS d 130 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 2 GLN h 73 ASN ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 47 HIS ** z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.147 160094 Z= 0.459 Angle : 0.839 15.644 239525 Z= 0.436 Chirality : 0.046 0.381 30521 Planarity : 0.008 0.138 12814 Dihedral : 23.723 179.979 80138 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.68 % Favored : 93.22 % Rotamer: Outliers : 5.14 % Allowed : 20.00 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.09 % 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: -1.10 (0.11), residues: 5767 helix: 0.34 (0.12), residues: 1890 sheet: -0.81 (0.15), residues: 1074 loop : -1.42 (0.11), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 23 HIS 0.013 0.002 HIS l 13 PHE 0.038 0.003 PHE Y 79 TYR 0.025 0.003 TYR R 51 ARG 0.009 0.001 ARG Y 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 887 time to evaluate : 6.568 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: B 161 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8641 (tt) REVERT: C 21 THR cc_start: 0.8034 (p) cc_final: 0.7660 (p) REVERT: C 63 SER cc_start: 0.7084 (t) cc_final: 0.6819 (p) REVERT: C 144 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6657 (mm) REVERT: C 154 SER cc_start: 0.8866 (t) cc_final: 0.8500 (p) REVERT: C 183 ASP cc_start: 0.8657 (t0) cc_final: 0.8023 (t70) REVERT: C 187 SER cc_start: 0.8696 (t) cc_final: 0.8345 (m) REVERT: C 192 THR cc_start: 0.8376 (m) cc_final: 0.8028 (p) REVERT: D 69 GLU cc_start: 0.8560 (tp30) cc_final: 0.8293 (tp30) REVERT: D 91 LEU cc_start: 0.7762 (mt) cc_final: 0.7405 (mt) REVERT: D 135 TYR cc_start: 0.7550 (t80) cc_final: 0.7203 (t80) REVERT: D 154 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6114 (mtm180) REVERT: E 20 ARG cc_start: 0.7157 (ttt180) cc_final: 0.6725 (ttt90) REVERT: E 146 ASN cc_start: 0.7602 (m-40) cc_final: 0.6856 (m-40) REVERT: E 147 MET cc_start: 0.7886 (ttp) cc_final: 0.7493 (ttp) REVERT: F 2 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7285 (mtp180) REVERT: G 129 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: I 18 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6101 (mtp180) REVERT: I 36 GLU cc_start: 0.6894 (mp0) cc_final: 0.6563 (pm20) REVERT: I 37 GLN cc_start: 0.7322 (pp30) cc_final: 0.6554 (pm20) REVERT: I 46 MET cc_start: 0.7250 (tpp) cc_final: 0.6742 (tpp) REVERT: I 88 MET cc_start: 0.5289 (OUTLIER) cc_final: 0.5003 (tpt) REVERT: I 112 GLU cc_start: 0.8337 (tt0) cc_final: 0.7851 (tt0) REVERT: J 49 PHE cc_start: 0.7895 (m-80) cc_final: 0.7455 (m-80) REVERT: K 20 VAL cc_start: 0.7973 (t) cc_final: 0.7680 (p) REVERT: K 40 ASN cc_start: 0.7618 (m110) cc_final: 0.7000 (m-40) REVERT: K 85 MET cc_start: 0.7691 (mtt) cc_final: 0.7478 (mtt) REVERT: K 86 VAL cc_start: 0.8021 (t) cc_final: 0.7643 (p) REVERT: L 15 LYS cc_start: 0.6819 (mmtm) cc_final: 0.6421 (mmmt) REVERT: L 78 SER cc_start: 0.8741 (m) cc_final: 0.8221 (m) REVERT: N 23 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7961 (tttt) REVERT: P 66 THR cc_start: 0.8368 (t) cc_final: 0.8063 (p) REVERT: P 76 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7384 (pttt) REVERT: Q 19 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7952 (mtmt) REVERT: S 65 GLU cc_start: 0.5783 (tp30) cc_final: 0.5500 (tp30) REVERT: T 70 ASN cc_start: 0.8068 (m-40) cc_final: 0.7480 (m110) REVERT: Y 5 PHE cc_start: 0.4095 (OUTLIER) cc_final: 0.3038 (p90) REVERT: Y 57 GLN cc_start: 0.8329 (pm20) cc_final: 0.8060 (pm20) REVERT: Y 120 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.6677 (m-80) REVERT: d 2 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.7793 (pt) REVERT: d 59 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7888 (ttm-80) REVERT: e 115 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7273 (mt0) REVERT: e 145 ASP cc_start: 0.5717 (OUTLIER) cc_final: 0.4852 (m-30) REVERT: e 184 ASP cc_start: 0.7454 (t0) cc_final: 0.6236 (m-30) REVERT: e 191 ASP cc_start: 0.7384 (t0) cc_final: 0.7163 (t0) REVERT: f 78 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7538 (ptpt) REVERT: f 142 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: f 161 LYS cc_start: 0.8135 (mmtp) cc_final: 0.7840 (tppp) REVERT: g 11 VAL cc_start: 0.6484 (OUTLIER) cc_final: 0.6204 (p) REVERT: g 42 GLU cc_start: 0.6398 (tp30) cc_final: 0.6106 (tp30) REVERT: g 153 ARG cc_start: 0.7101 (mtp85) cc_final: 0.6821 (ttm170) REVERT: h 60 GLU cc_start: 0.4039 (mt-10) cc_final: 0.3554 (tt0) REVERT: h 91 PHE cc_start: 0.1942 (OUTLIER) cc_final: 0.0998 (t80) REVERT: h 132 PHE cc_start: 0.7613 (m-80) cc_final: 0.7020 (m-80) REVERT: j 32 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7753 (m-80) REVERT: j 56 ASP cc_start: 0.7670 (m-30) cc_final: 0.7404 (m-30) REVERT: j 82 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8658 (m-40) REVERT: j 106 GLU cc_start: 0.7562 (mp0) cc_final: 0.7306 (mp0) REVERT: j 113 MET cc_start: 0.6763 (mmm) cc_final: 0.6287 (mmm) REVERT: k 143 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7064 (tm-30) REVERT: n 80 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7014 (pt0) REVERT: p 11 ARG cc_start: 0.7917 (tpm170) cc_final: 0.7422 (tpp80) REVERT: p 52 GLN cc_start: 0.8812 (mt0) cc_final: 0.8551 (mt0) REVERT: q 23 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7774 (mm-30) REVERT: r 67 ASP cc_start: 0.7256 (t0) cc_final: 0.6516 (p0) REVERT: s 1 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5978 (tpt) REVERT: s 21 SER cc_start: 0.7837 (m) cc_final: 0.7566 (p) REVERT: t 9 ASP cc_start: 0.7883 (m-30) cc_final: 0.7113 (t0) REVERT: t 86 ARG cc_start: 0.7778 (mtm110) cc_final: 0.7538 (ttp-110) REVERT: t 87 PHE cc_start: 0.7167 (m-80) cc_final: 0.6759 (m-80) REVERT: u 10 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7853 (pttm) REVERT: v 68 LYS cc_start: 0.7391 (tptp) cc_final: 0.6939 (tttp) REVERT: v 70 GLU cc_start: 0.7641 (pm20) cc_final: 0.7186 (pm20) REVERT: z 48 TYR cc_start: 0.8215 (m-80) cc_final: 0.8005 (m-80) REVERT: 2 52 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7281 (tppt) outliers start: 247 outliers final: 185 residues processed: 1049 average time/residue: 1.5241 time to fit residues: 2817.6054 Evaluate side-chains 1049 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 845 time to evaluate : 6.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 24 GLU Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 10 PHE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 107 THR Chi-restraints excluded: chain Y residue 109 THR Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 120 PHE Chi-restraints excluded: chain Y residue 128 ARG Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 199 GLU Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 252 THR Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain e residue 175 ILE Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 38 MET Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 11 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 72 LEU Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 141 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 47 ILE Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 148 VAL Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain l residue 181 ILE Chi-restraints excluded: chain l residue 187 THR Chi-restraints excluded: chain l residue 191 MET Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain m residue 97 ILE Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 87 ILE Chi-restraints excluded: chain n residue 89 ASP Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain p residue 75 SER Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 92 ARG Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 92 ASN Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 77 THR Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 60 VAL Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 51 VAL Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 33 THR Chi-restraints excluded: chain z residue 40 ARG Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 4 residue 13 THR Chi-restraints excluded: chain 4 residue 37 CYS Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 615 optimal weight: 3.9990 chunk 397 optimal weight: 4.9990 chunk 594 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 632 optimal weight: 20.0000 chunk 677 optimal weight: 6.9990 chunk 491 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 781 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS G 130 ASN ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN p 20 GLN ** z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 160094 Z= 0.200 Angle : 0.647 14.475 239525 Z= 0.351 Chirality : 0.036 0.389 30521 Planarity : 0.006 0.127 12814 Dihedral : 23.627 179.912 80138 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.36 % Favored : 94.57 % Rotamer: Outliers : 3.79 % Allowed : 21.58 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 5767 helix: 0.83 (0.12), residues: 1894 sheet: -0.65 (0.16), residues: 1038 loop : -1.29 (0.11), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 42 HIS 0.009 0.001 HIS B 18 PHE 0.027 0.002 PHE H 49 TYR 0.023 0.002 TYR r 38 ARG 0.009 0.000 ARG j 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 877 time to evaluate : 6.413 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: B 161 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8497 (tt) REVERT: C 21 THR cc_start: 0.8160 (p) cc_final: 0.7790 (p) REVERT: C 63 SER cc_start: 0.7093 (t) cc_final: 0.6820 (p) REVERT: C 143 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7066 (ttp80) REVERT: C 144 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6433 (mm) REVERT: C 154 SER cc_start: 0.8755 (t) cc_final: 0.8413 (p) REVERT: C 182 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8603 (mm) REVERT: C 187 SER cc_start: 0.8644 (t) cc_final: 0.8333 (m) REVERT: C 192 THR cc_start: 0.8164 (m) cc_final: 0.7847 (p) REVERT: D 69 GLU cc_start: 0.8476 (tp30) cc_final: 0.7921 (tp30) REVERT: D 91 LEU cc_start: 0.7711 (mt) cc_final: 0.7356 (mt) REVERT: D 135 TYR cc_start: 0.7528 (t80) cc_final: 0.7180 (t80) REVERT: D 154 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6247 (mtm180) REVERT: E 20 ARG cc_start: 0.7210 (ttt180) cc_final: 0.6816 (ttt90) REVERT: E 78 ASN cc_start: 0.8186 (t0) cc_final: 0.7349 (p0) REVERT: E 146 ASN cc_start: 0.7458 (m-40) cc_final: 0.6691 (m-40) REVERT: E 147 MET cc_start: 0.7758 (ttp) cc_final: 0.7271 (ttp) REVERT: F 2 ARG cc_start: 0.7506 (mtp85) cc_final: 0.7258 (mtp180) REVERT: G 40 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6724 (pt0) REVERT: H 27 MET cc_start: 0.7212 (ptp) cc_final: 0.6977 (ptp) REVERT: H 38 ASN cc_start: 0.7290 (m-40) cc_final: 0.6448 (m110) REVERT: I 37 GLN cc_start: 0.6982 (pp30) cc_final: 0.6459 (pm20) REVERT: I 46 MET cc_start: 0.7221 (tpp) cc_final: 0.6737 (tpp) REVERT: I 112 GLU cc_start: 0.8216 (tt0) cc_final: 0.7790 (tt0) REVERT: K 85 MET cc_start: 0.7365 (mtt) cc_final: 0.7139 (mtt) REVERT: K 86 VAL cc_start: 0.7947 (t) cc_final: 0.7484 (p) REVERT: L 6 GLN cc_start: 0.8436 (mt0) cc_final: 0.8229 (mt0) REVERT: L 15 LYS cc_start: 0.6773 (mmtm) cc_final: 0.6339 (mmmt) REVERT: L 78 SER cc_start: 0.8603 (m) cc_final: 0.8159 (m) REVERT: L 81 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8316 (mp) REVERT: L 94 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8129 (mtt-85) REVERT: L 115 SER cc_start: 0.8898 (p) cc_final: 0.8672 (p) REVERT: N 23 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7921 (tttt) REVERT: P 66 THR cc_start: 0.8273 (t) cc_final: 0.7991 (p) REVERT: P 76 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7358 (pttt) REVERT: Q 19 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8066 (mtmt) REVERT: Q 27 ARG cc_start: 0.7364 (ptt-90) cc_final: 0.7137 (ptt90) REVERT: S 65 GLU cc_start: 0.5596 (tp30) cc_final: 0.5315 (tp30) REVERT: T 70 ASN cc_start: 0.7968 (m-40) cc_final: 0.7393 (m110) REVERT: U 4 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7201 (mm) REVERT: U 33 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7443 (mtt-85) REVERT: c 264 ASP cc_start: 0.8246 (m-30) cc_final: 0.7886 (m-30) REVERT: e 115 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7361 (mt0) REVERT: e 145 ASP cc_start: 0.5871 (OUTLIER) cc_final: 0.5011 (m-30) REVERT: e 184 ASP cc_start: 0.7308 (t0) cc_final: 0.6114 (m-30) REVERT: e 191 ASP cc_start: 0.7291 (t0) cc_final: 0.7054 (t0) REVERT: f 78 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7472 (ptpt) REVERT: f 134 GLU cc_start: 0.7817 (tp30) cc_final: 0.6832 (tp30) REVERT: f 142 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6548 (m-30) REVERT: f 161 LYS cc_start: 0.8123 (mmtp) cc_final: 0.7835 (tppp) REVERT: g 42 GLU cc_start: 0.6536 (tp30) cc_final: 0.6272 (tp30) REVERT: g 114 ASP cc_start: 0.8425 (t0) cc_final: 0.7899 (m-30) REVERT: h 91 PHE cc_start: 0.1775 (OUTLIER) cc_final: 0.0746 (t80) REVERT: i 136 GLN cc_start: 0.8258 (mt0) cc_final: 0.7816 (mt0) REVERT: j 32 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: j 56 ASP cc_start: 0.7645 (m-30) cc_final: 0.7400 (m-30) REVERT: j 82 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8492 (m-40) REVERT: j 113 MET cc_start: 0.6759 (mmm) cc_final: 0.6457 (mmm) REVERT: k 143 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7083 (tm-30) REVERT: n 80 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7013 (pt0) REVERT: o 112 GLU cc_start: 0.8136 (tp30) cc_final: 0.7647 (tp30) REVERT: p 11 ARG cc_start: 0.7860 (tpm170) cc_final: 0.7397 (tpp80) REVERT: q 23 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7714 (mm-30) REVERT: r 67 ASP cc_start: 0.7238 (t0) cc_final: 0.6468 (p0) REVERT: r 95 ARG cc_start: 0.8504 (ttp-170) cc_final: 0.7929 (ttt180) REVERT: s 21 SER cc_start: 0.8018 (m) cc_final: 0.7720 (p) REVERT: t 9 ASP cc_start: 0.7867 (m-30) cc_final: 0.7124 (t0) REVERT: t 87 PHE cc_start: 0.7046 (m-80) cc_final: 0.6725 (m-80) REVERT: u 10 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7855 (pttm) REVERT: u 57 TYR cc_start: 0.8306 (m-80) cc_final: 0.8066 (m-80) REVERT: v 29 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7441 (mt-10) REVERT: v 68 LYS cc_start: 0.7312 (tptp) cc_final: 0.6924 (tttp) REVERT: v 70 GLU cc_start: 0.7680 (pm20) cc_final: 0.7389 (pm20) REVERT: 0 30 LYS cc_start: 0.8070 (mptt) cc_final: 0.7834 (mttp) outliers start: 182 outliers final: 134 residues processed: 998 average time/residue: 1.3120 time to fit residues: 2253.9981 Evaluate side-chains 992 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 842 time to evaluate : 8.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 109 THR Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 199 GLU Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 38 MET Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain l residue 181 ILE Chi-restraints excluded: chain l residue 187 THR Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 87 ILE Chi-restraints excluded: chain n residue 89 ASP Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 75 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain s residue 92 ASN Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 77 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 51 VAL Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain x residue 39 GLN Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 33 THR Chi-restraints excluded: chain z residue 40 ARG Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 4 residue 13 THR Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 904 optimal weight: 2.9990 chunk 952 optimal weight: 3.9990 chunk 869 optimal weight: 10.0000 chunk 926 optimal weight: 2.9990 chunk 557 optimal weight: 10.0000 chunk 403 optimal weight: 2.9990 chunk 727 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 837 optimal weight: 0.9990 chunk 876 optimal weight: 3.9990 chunk 923 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS D 140 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Y 161 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 20 GLN ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 160094 Z= 0.255 Angle : 0.658 14.583 239525 Z= 0.354 Chirality : 0.037 0.382 30521 Planarity : 0.006 0.130 12814 Dihedral : 23.574 179.056 80136 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.96 % Favored : 93.97 % Rotamer: Outliers : 3.93 % Allowed : 22.02 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 5767 helix: 0.87 (0.12), residues: 1892 sheet: -0.61 (0.16), residues: 1038 loop : -1.28 (0.11), residues: 2837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 95 HIS 0.008 0.001 HIS l 13 PHE 0.041 0.002 PHE Y 79 TYR 0.027 0.002 TYR D 103 ARG 0.009 0.000 ARG j 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 866 time to evaluate : 5.963 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: B 161 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8525 (tt) REVERT: C 21 THR cc_start: 0.8102 (p) cc_final: 0.7711 (p) REVERT: C 63 SER cc_start: 0.7055 (t) cc_final: 0.6750 (p) REVERT: C 143 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7124 (ttp80) REVERT: C 144 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6533 (mm) REVERT: C 154 SER cc_start: 0.8688 (t) cc_final: 0.8406 (p) REVERT: C 182 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8597 (mm) REVERT: C 183 ASP cc_start: 0.8617 (t0) cc_final: 0.7935 (t70) REVERT: C 187 SER cc_start: 0.8622 (t) cc_final: 0.8321 (m) REVERT: C 192 THR cc_start: 0.8138 (m) cc_final: 0.7809 (p) REVERT: D 69 GLU cc_start: 0.8497 (tp30) cc_final: 0.7935 (tp30) REVERT: D 91 LEU cc_start: 0.7751 (mt) cc_final: 0.7389 (mt) REVERT: D 135 TYR cc_start: 0.7530 (t80) cc_final: 0.7188 (t80) REVERT: D 154 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6200 (mtm180) REVERT: E 78 ASN cc_start: 0.8298 (t0) cc_final: 0.7472 (p0) REVERT: E 146 ASN cc_start: 0.7469 (m-40) cc_final: 0.6714 (m-40) REVERT: E 147 MET cc_start: 0.7776 (ttp) cc_final: 0.7321 (ttp) REVERT: F 2 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7278 (mtp180) REVERT: G 40 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6802 (pt0) REVERT: H 27 MET cc_start: 0.7168 (ptp) cc_final: 0.6950 (ptp) REVERT: H 38 ASN cc_start: 0.7270 (m-40) cc_final: 0.6427 (m110) REVERT: I 18 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6010 (mtp180) REVERT: I 37 GLN cc_start: 0.7018 (pp30) cc_final: 0.6550 (pm20) REVERT: I 46 MET cc_start: 0.7228 (tpp) cc_final: 0.6752 (tpp) REVERT: I 112 GLU cc_start: 0.8235 (tt0) cc_final: 0.7798 (tt0) REVERT: K 85 MET cc_start: 0.7346 (mtt) cc_final: 0.7070 (mtt) REVERT: K 86 VAL cc_start: 0.7943 (t) cc_final: 0.7469 (p) REVERT: L 15 LYS cc_start: 0.6808 (mmtm) cc_final: 0.6357 (mmmt) REVERT: L 78 SER cc_start: 0.8613 (m) cc_final: 0.8162 (m) REVERT: L 81 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8311 (mp) REVERT: L 94 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8144 (mtt-85) REVERT: L 115 SER cc_start: 0.8910 (p) cc_final: 0.8683 (p) REVERT: P 66 THR cc_start: 0.8271 (t) cc_final: 0.7975 (p) REVERT: P 76 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7356 (pttt) REVERT: T 70 ASN cc_start: 0.7986 (m-40) cc_final: 0.7411 (m110) REVERT: U 4 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7206 (mm) REVERT: U 58 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5053 (mttt) REVERT: Y 128 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7869 (tmm160) REVERT: Y 170 ARG cc_start: 0.6077 (ptt-90) cc_final: 0.5328 (ttt-90) REVERT: c 264 ASP cc_start: 0.8268 (m-30) cc_final: 0.7906 (m-30) REVERT: e 115 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7377 (mt0) REVERT: e 145 ASP cc_start: 0.5909 (OUTLIER) cc_final: 0.4994 (m-30) REVERT: e 184 ASP cc_start: 0.7336 (t0) cc_final: 0.6114 (m-30) REVERT: e 191 ASP cc_start: 0.7308 (t0) cc_final: 0.7085 (t0) REVERT: f 78 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7481 (ptpt) REVERT: f 134 GLU cc_start: 0.7837 (tp30) cc_final: 0.6855 (tp30) REVERT: f 142 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: f 161 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7839 (tppp) REVERT: g 42 GLU cc_start: 0.6507 (tp30) cc_final: 0.6259 (tp30) REVERT: g 114 ASP cc_start: 0.8405 (t0) cc_final: 0.7867 (m-30) REVERT: g 141 ILE cc_start: 0.8058 (tp) cc_final: 0.7833 (pt) REVERT: h 91 PHE cc_start: 0.1825 (OUTLIER) cc_final: 0.0843 (t80) REVERT: j 32 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: j 56 ASP cc_start: 0.7637 (m-30) cc_final: 0.7382 (m-30) REVERT: j 82 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8513 (m-40) REVERT: j 113 MET cc_start: 0.6817 (mmm) cc_final: 0.6510 (mmm) REVERT: k 143 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7160 (tm-30) REVERT: n 80 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7027 (pt0) REVERT: p 11 ARG cc_start: 0.7853 (tpm170) cc_final: 0.7400 (tpp80) REVERT: q 23 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7575 (mm-30) REVERT: r 95 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.7902 (ttt180) REVERT: s 21 SER cc_start: 0.8023 (m) cc_final: 0.7723 (p) REVERT: t 87 PHE cc_start: 0.7215 (m-80) cc_final: 0.6795 (m-10) REVERT: u 10 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7871 (pttm) REVERT: v 29 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7601 (mt-10) REVERT: v 68 LYS cc_start: 0.7325 (tptp) cc_final: 0.6922 (tttp) REVERT: v 70 GLU cc_start: 0.7670 (pm20) cc_final: 0.7379 (pm20) REVERT: 0 30 LYS cc_start: 0.8097 (mptt) cc_final: 0.7842 (mttp) REVERT: 2 52 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6683 (ptpp) outliers start: 189 outliers final: 152 residues processed: 988 average time/residue: 1.3309 time to fit residues: 2266.6067 Evaluate side-chains 1023 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 853 time to evaluate : 6.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 11 CYS Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 109 THR Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 128 ARG Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 199 GLU Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 38 MET Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain l residue 181 ILE Chi-restraints excluded: chain l residue 187 THR Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 87 ILE Chi-restraints excluded: chain n residue 89 ASP Chi-restraints excluded: chain o residue 19 SER Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 75 SER Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 77 THR Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 51 VAL Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain x residue 39 GLN Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 33 THR Chi-restraints excluded: chain z residue 40 ARG Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 2 residue 55 LEU Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 4 residue 13 THR Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 608 optimal weight: 8.9990 chunk 980 optimal weight: 0.5980 chunk 598 optimal weight: 8.9990 chunk 464 optimal weight: 8.9990 chunk 681 optimal weight: 8.9990 chunk 1028 optimal weight: 10.0000 chunk 946 optimal weight: 0.8980 chunk 818 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 632 optimal weight: 20.0000 chunk 502 optimal weight: 20.0000 overall best weight: 5.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS D 140 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN p 20 GLN ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 160094 Z= 0.448 Angle : 0.812 15.323 239525 Z= 0.422 Chirality : 0.044 0.376 30521 Planarity : 0.007 0.138 12814 Dihedral : 23.669 179.573 80134 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.04 % Favored : 92.86 % Rotamer: Outliers : 4.14 % Allowed : 21.98 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.11), residues: 5767 helix: 0.37 (0.12), residues: 1897 sheet: -0.93 (0.15), residues: 1077 loop : -1.52 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 23 HIS 0.013 0.002 HIS l 13 PHE 0.049 0.003 PHE Y 79 TYR 0.025 0.003 TYR D 103 ARG 0.008 0.001 ARG j 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 836 time to evaluate : 6.587 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: B 161 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8637 (tt) REVERT: C 21 THR cc_start: 0.8057 (p) cc_final: 0.7661 (p) REVERT: C 143 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7054 (ttp80) REVERT: C 144 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6488 (mm) REVERT: C 154 SER cc_start: 0.8752 (t) cc_final: 0.8453 (p) REVERT: C 182 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8644 (mm) REVERT: C 183 ASP cc_start: 0.8663 (t0) cc_final: 0.8012 (t70) REVERT: C 187 SER cc_start: 0.8641 (t) cc_final: 0.8290 (m) REVERT: C 192 THR cc_start: 0.8365 (m) cc_final: 0.8016 (p) REVERT: D 69 GLU cc_start: 0.8526 (tp30) cc_final: 0.8245 (tp30) REVERT: D 91 LEU cc_start: 0.7734 (mt) cc_final: 0.7365 (mt) REVERT: D 154 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.6111 (mtm180) REVERT: E 20 ARG cc_start: 0.7171 (ttt180) cc_final: 0.6926 (ttt90) REVERT: E 146 ASN cc_start: 0.7590 (m-40) cc_final: 0.6837 (m-40) REVERT: E 147 MET cc_start: 0.7825 (ttp) cc_final: 0.7409 (ttp) REVERT: F 2 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7267 (mtp180) REVERT: G 78 ARG cc_start: 0.5593 (ttt180) cc_final: 0.5270 (ttm-80) REVERT: H 27 MET cc_start: 0.7223 (ptp) cc_final: 0.6917 (ptp) REVERT: I 18 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6069 (mtp180) REVERT: I 37 GLN cc_start: 0.6918 (pp30) cc_final: 0.6637 (pm20) REVERT: I 46 MET cc_start: 0.7271 (tpp) cc_final: 0.6754 (tpp) REVERT: I 95 ARG cc_start: 0.5787 (ttm-80) cc_final: 0.5320 (mtp85) REVERT: I 112 GLU cc_start: 0.8359 (tt0) cc_final: 0.7895 (tt0) REVERT: J 49 PHE cc_start: 0.7846 (m-80) cc_final: 0.7469 (m-80) REVERT: K 40 ASN cc_start: 0.7402 (m110) cc_final: 0.6830 (m-40) REVERT: K 85 MET cc_start: 0.7641 (mtt) cc_final: 0.7418 (mtt) REVERT: K 86 VAL cc_start: 0.8036 (t) cc_final: 0.7581 (p) REVERT: L 15 LYS cc_start: 0.6842 (mmtm) cc_final: 0.6312 (mmmt) REVERT: L 43 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7314 (mtpp) REVERT: L 78 SER cc_start: 0.8725 (m) cc_final: 0.8245 (m) REVERT: L 81 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8312 (mp) REVERT: L 94 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8207 (mtt-85) REVERT: O 83 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7076 (mm-30) REVERT: P 66 THR cc_start: 0.8346 (t) cc_final: 0.8051 (p) REVERT: P 76 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7353 (pttt) REVERT: Q 19 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7925 (mtmt) REVERT: Q 81 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7275 (mttm) REVERT: S 65 GLU cc_start: 0.5865 (tp30) cc_final: 0.5343 (tp30) REVERT: T 70 ASN cc_start: 0.8028 (m-40) cc_final: 0.7457 (m110) REVERT: U 58 LYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5162 (mttt) REVERT: d 2 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8005 (pt) REVERT: d 59 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7756 (ttm-80) REVERT: e 115 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7306 (mt0) REVERT: e 145 ASP cc_start: 0.5864 (OUTLIER) cc_final: 0.5504 (m-30) REVERT: f 78 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7608 (ptpt) REVERT: f 142 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: f 161 LYS cc_start: 0.8115 (mmtp) cc_final: 0.7823 (tppp) REVERT: g 42 GLU cc_start: 0.6569 (tp30) cc_final: 0.6296 (tp30) REVERT: h 91 PHE cc_start: 0.2057 (OUTLIER) cc_final: 0.1102 (t80) REVERT: j 32 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: j 56 ASP cc_start: 0.7668 (m-30) cc_final: 0.7396 (m-30) REVERT: j 82 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8598 (m-40) REVERT: j 97 THR cc_start: 0.8371 (p) cc_final: 0.7592 (t) REVERT: j 113 MET cc_start: 0.6907 (mmm) cc_final: 0.6531 (mmm) REVERT: k 143 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7092 (tm-30) REVERT: n 80 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7020 (pt0) REVERT: p 11 ARG cc_start: 0.7907 (tpm170) cc_final: 0.7389 (tpp80) REVERT: q 23 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7782 (mm-30) REVERT: r 95 ARG cc_start: 0.8563 (ttp-170) cc_final: 0.7919 (ttt180) REVERT: s 1 MET cc_start: 0.6487 (tpt) cc_final: 0.6078 (tpt) REVERT: s 21 SER cc_start: 0.7918 (m) cc_final: 0.7641 (p) REVERT: s 92 ASN cc_start: 0.6608 (OUTLIER) cc_final: 0.6361 (p0) REVERT: t 9 ASP cc_start: 0.7907 (m-30) cc_final: 0.7152 (t0) REVERT: t 87 PHE cc_start: 0.7154 (m-80) cc_final: 0.6767 (m-80) REVERT: u 9 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.5192 (mtm-85) REVERT: u 10 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7845 (pttm) REVERT: v 70 GLU cc_start: 0.7664 (pm20) cc_final: 0.7200 (pm20) REVERT: 0 51 GLU cc_start: 0.7125 (tt0) cc_final: 0.6858 (tt0) REVERT: 2 52 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7205 (tppt) outliers start: 199 outliers final: 164 residues processed: 964 average time/residue: 1.3130 time to fit residues: 2176.0896 Evaluate side-chains 1007 residues out of total 4805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 824 time to evaluate : 6.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 66 PHE Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 25 ASN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 94 ARG Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 80 SER Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 13 SER Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain R residue 9 LYS Chi-restraints excluded: chain R residue 11 CYS Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 34 LYS Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 25 ARG Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 109 THR Chi-restraints excluded: chain Y residue 113 ASN Chi-restraints excluded: chain Y residue 130 PHE Chi-restraints excluded: chain Y residue 137 ASP Chi-restraints excluded: chain c residue 36 LYS Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 199 GLU Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain d residue 2 ILE Chi-restraints excluded: chain d residue 73 VAL Chi-restraints excluded: chain d residue 97 SER Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 38 MET Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 83 TYR Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 144 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 60 ASP Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 17 ASP Chi-restraints excluded: chain h residue 87 GLU Chi-restraints excluded: chain h residue 91 PHE Chi-restraints excluded: chain h residue 108 VAL Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 70 THR Chi-restraints excluded: chain j residue 28 SER Chi-restraints excluded: chain j residue 32 TYR Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 116 ILE Chi-restraints excluded: chain k residue 12 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 151 ILE Chi-restraints excluded: chain l residue 181 ILE Chi-restraints excluded: chain l residue 187 THR Chi-restraints excluded: chain l residue 191 MET Chi-restraints excluded: chain m residue 6 SER Chi-restraints excluded: chain m residue 65 LEU Chi-restraints excluded: chain m residue 89 SER Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 87 ILE Chi-restraints excluded: chain n residue 89 ASP Chi-restraints excluded: chain p residue 20 GLN Chi-restraints excluded: chain p residue 75 SER Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 55 ASP Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain s residue 92 ASN Chi-restraints excluded: chain t residue 12 ILE Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 30 SER Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 77 THR Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 ARG Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain v residue 51 VAL Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain w residue 19 SER Chi-restraints excluded: chain w residue 22 LEU Chi-restraints excluded: chain w residue 25 THR Chi-restraints excluded: chain w residue 35 SER Chi-restraints excluded: chain x residue 39 GLN Chi-restraints excluded: chain y residue 7 ILE Chi-restraints excluded: chain z residue 22 LEU Chi-restraints excluded: chain z residue 33 THR Chi-restraints excluded: chain z residue 40 ARG Chi-restraints excluded: chain 0 residue 12 VAL Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 2 residue 54 ASP Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 13 THR Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 4 residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1032 random chunks: chunk 650 optimal weight: 5.9990 chunk 872 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 754 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 227 optimal weight: 0.3980 chunk 820 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 842 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS G 130 ASN I 25 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN p 20 GLN ** z 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103625 restraints weight = 259423.289| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 0.80 r_work: 0.3101 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 160094 Z= 0.161 Angle : 0.619 14.052 239525 Z= 0.338 Chirality : 0.035 0.396 30521 Planarity : 0.006 0.123 12814 Dihedral : 23.610 179.722 80134 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 3.10 % Allowed : 22.93 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 5767 helix: 0.94 (0.12), residues: 1891 sheet: -0.59 (0.16), residues: 1031 loop : -1.29 (0.11), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 42 HIS 0.005 0.001 HIS l 13 PHE 0.032 0.001 PHE Y 79 TYR 0.028 0.002 TYR D 103 ARG 0.009 0.000 ARG j 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38474.07 seconds wall clock time: 673 minutes 48.48 seconds (40428.48 seconds total)