Starting phenix.real_space_refine on Sun Apr 14 04:52:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6y_29788/04_2024/8g6y_29788_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6y_29788/04_2024/8g6y_29788.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6y_29788/04_2024/8g6y_29788_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6y_29788/04_2024/8g6y_29788_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6y_29788/04_2024/8g6y_29788_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6y_29788/04_2024/8g6y_29788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6y_29788/04_2024/8g6y_29788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6y_29788/04_2024/8g6y_29788_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6y_29788/04_2024/8g6y_29788_updated.pdb" } resolution = 2.09 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= 0.001 sd= 0.007 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: 8 Type Number sf(0) Gaussians K 15 8.98 5 Zn 2 6.06 5 P 3036 5.49 5 Mg 231 5.21 5 S 82 5.16 5 C 44623 2.51 5 N 16780 2.21 5 O 28914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 7": "OE1" <-> "OE2" Residue "0 ARG 44": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 33": "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 "c GLU 23": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" 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 "c ARG 212": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d GLU 81": "OE1" <-> "OE2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ARG 128": "NH1" <-> "NH2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d GLU 183": "OE1" <-> "OE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e GLU 152": "OE1" <-> "OE2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "f GLU 11": "OE1" <-> "OE2" Residue "f GLU 42": "OE1" <-> "OE2" 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 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g GLU 130": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j GLU 110": "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 ARG 60": "NH1" <-> "NH2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m GLU 74": "OE1" <-> "OE2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "n GLU 60": "OE1" <-> "OE2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "n GLU 112": "OE1" <-> "OE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p GLU 89": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q GLU 34": "OE1" <-> "OE2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r ARG 110": "NH1" <-> "NH2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s GLU 54": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "s GLU 89": "OE1" <-> "OE2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t GLU 37": "OE1" <-> "OE2" Residue "t GLU 60": "OE1" <-> "OE2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 55": "OE1" <-> "OE2" Residue "u PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u GLU 69": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 8": "OE1" <-> "OE2" Residue "x GLU 24": "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 GLU 39": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ARG 52": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 93683 Number of models: 1 Model: "" Number of chains: 69 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: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "X" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 317 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 12} Chain: "Y" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1578 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 13, 'rna3p': 60} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1601 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 9, 'rna3p': 65} Chain: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 7, 'rna2p_pur': 266, 'rna2p_pyr': 140, 'rna3p': 17, 'rna3p_pur': 1319, 'rna3p_pyr': 1004} Link IDs: {'rna2p': 412, 'rna3p': 2340} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 58, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 106} 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: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} 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 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " 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: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 576 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "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} Chain: "Y" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'YRW': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'8AN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 237 Unusual residues: {' K': 13, ' MG': 224} Classifications: {'undetermined': 237} Link IDs: {None: 236} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "c" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "1" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "2" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3019, 3019 Classifications: {'water': 3019} Link IDs: {None: 3018} Chain: "b" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "d" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "i" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "j" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "k" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "l" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "m" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "o" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "p" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "q" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "r" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "s" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "u" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "v" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "w" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1383 SG CYS 3 11 157.323 85.533 164.739 1.00 19.19 S ATOM 1408 SG CYS 3 14 155.053 83.454 162.296 1.00 15.94 S ATOM 1511 SG CYS 3 27 154.246 83.793 166.000 1.00 16.17 S ATOM 1730 SG CYS 4 16 208.743 155.107 93.530 1.00 39.27 S ATOM 1742 SG CYS 4 18 211.564 155.913 96.124 1.00 40.02 S ATOM 1884 SG CYS 4 37 210.582 152.105 94.982 1.00 43.25 S ATOM 1905 SG CYS 4 40 209.051 154.139 97.427 1.00 42.83 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P U a2491 " occ=0.50 ... (18 atoms not shown) pdb=" C6 U a2491 " occ=0.50 residue: pdb=" P U a2492 " occ=0.50 ... (18 atoms not shown) pdb=" C6 U a2492 " occ=0.50 Time building chain proxies: 38.41, per 1000 atoms: 0.41 Number of scatterers: 93683 At special positions: 0 Unit cell: (233.192, 201.056, 206, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 15 19.00 S 82 16.00 P 3036 15.00 Mg 231 11.99 O 28914 8.00 N 16780 7.00 C 44623 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 44.81 Conformation dependent library (CDL) restraints added in 3.7 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 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " 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 18 " Number of angles added : 9 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 48 sheets defined 26.6% alpha, 19.9% beta 1052 base pairs and 1496 stacking pairs defined. Time for finding SS restraints: 45.38 Creating SS restraints... Processing helix chain '1' and resid 9 through 16 Processing helix chain '1' and resid 18 through 22 Processing helix chain '1' and resid 25 through 37 Processing helix chain '2' and resid 8 through 11 No H-bonds generated for 'chain '2' and resid 8 through 11' Processing helix chain '2' and resid 38 through 45 Processing helix chain '2' and resid 52 through 61 removed outlier: 4.425A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 33 No H-bonds generated for 'chain '3' and resid 31 through 33' Processing helix chain '4' and resid 38 through 40 No H-bonds generated for 'chain '4' and resid 38 through 40' Processing helix chain '4' and resid 42 through 45 No H-bonds generated for 'chain '4' and resid 42 through 45' Processing helix chain '4' and resid 56 through 63 Processing helix chain 'c' and resid 31 through 33 No H-bonds generated for 'chain 'c' and resid 31 through 33' Processing helix chain 'c' and resid 198 through 202 removed outlier: 4.172A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 208 through 214 removed outlier: 3.599A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 222 through 224 No H-bonds generated for 'chain 'c' and resid 222 through 224' Processing helix chain 'c' and resid 264 through 266 No H-bonds generated for 'chain 'c' and resid 264 through 266' Processing helix chain 'd' and resid 57 through 59 No H-bonds generated for 'chain 'd' and resid 57 through 59' Processing helix chain 'd' and resid 62 through 71 Processing helix chain 'd' and resid 98 through 101 Processing helix chain 'd' and resid 121 through 125 Processing helix chain 'e' and resid 16 through 19 No H-bonds generated for 'chain 'e' and resid 16 through 19' Processing helix chain 'e' and resid 25 through 38 Processing helix chain 'e' and resid 98 through 115 Processing helix chain 'e' and resid 131 through 141 Processing helix chain 'e' and resid 155 through 162 Processing helix chain 'e' and resid 172 through 174 No H-bonds generated for 'chain 'e' and resid 172 through 174' Processing helix chain 'e' and resid 177 through 182 Processing helix chain 'e' and resid 190 through 199 Processing helix chain 'f' and resid 3 through 20 removed outlier: 5.297A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 61 removed outlier: 3.734A pdb=" N ALA f 55 " --> pdb=" O ASP f 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 94 through 105 removed outlier: 3.599A pdb=" N ARG f 102 " --> pdb=" O GLU f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 108 through 110 No H-bonds generated for 'chain 'f' and resid 108 through 110' Processing helix chain 'f' and resid 135 through 137 No H-bonds generated for 'chain 'f' and resid 135 through 137' Processing helix chain 'f' and resid 163 through 173 removed outlier: 3.716A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 80 Processing helix chain 'g' and resid 138 through 151 Processing helix chain 'h' and resid 23 through 28 Processing helix chain 'h' and resid 31 through 33 No H-bonds generated for 'chain 'h' and resid 31 through 33' Processing helix chain 'i' and resid 25 through 37 removed outlier: 3.750A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 59 through 61 No H-bonds generated for 'chain 'i' and resid 59 through 61' Processing helix chain 'i' and resid 68 through 71 No H-bonds generated for 'chain 'i' and resid 68 through 71' Processing helix chain 'i' and resid 89 through 108 Proline residue: i 97 - end of helix removed outlier: 4.214A pdb=" N VAL i 100 " --> pdb=" O ARG i 96 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 121 removed outlier: 3.941A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 133 through 135 No H-bonds generated for 'chain 'i' and resid 133 through 135' Processing helix chain 'j' and resid 105 through 107 No H-bonds generated for 'chain 'j' and resid 105 through 107' Processing helix chain 'j' and resid 110 through 118 removed outlier: 3.656A pdb=" N MET j 113 " --> pdb=" O GLU j 110 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYS j 114 " --> pdb=" O LYS j 111 " (cutoff:3.500A) Processing helix chain 'k' and resid 38 through 40 No H-bonds generated for 'chain 'k' and resid 38 through 40' Processing helix chain 'k' and resid 57 through 60 No H-bonds generated for 'chain 'k' and resid 57 through 60' Processing helix chain 'k' and resid 71 through 73 No H-bonds generated for 'chain 'k' and resid 71 through 73' Processing helix chain 'k' and resid 79 through 84 removed outlier: 4.342A pdb=" N ALA k 83 " --> pdb=" O SER k 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 97 Processing helix chain 'k' and resid 129 through 138 Processing helix chain 'l' and resid 43 through 56 Processing helix chain 'l' and resid 110 through 123 removed outlier: 3.977A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 31 Processing helix chain 'm' and resid 38 through 56 removed outlier: 4.187A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix Processing helix chain 'm' and resid 60 through 68 Processing helix chain 'm' and resid 73 through 86 removed outlier: 4.869A 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 3 through 21 removed outlier: 4.531A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 5.074A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 68 through 85 removed outlier: 3.517A pdb=" N LYS n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 113 Processing helix chain 'o' and resid 3 through 12 removed outlier: 3.889A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 56 No H-bonds generated for 'chain 'o' and resid 54 through 56' Processing helix chain 'o' and resid 98 through 102 Processing helix chain 'o' and resid 105 through 108 Processing helix chain 'p' and resid 7 through 20 Processing helix chain 'p' and resid 26 through 29 Processing helix chain 'p' and resid 32 through 71 removed outlier: 3.507A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 86 Processing helix chain 'p' and resid 92 through 101 Processing helix chain 'p' and resid 103 through 117 Processing helix chain 'r' and resid 14 through 24 removed outlier: 3.888A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 37 Processing helix chain 'r' and resid 42 through 60 Processing helix chain 'r' and resid 66 through 68 No H-bonds generated for 'chain 'r' and resid 66 through 68' Processing helix chain 'r' and resid 89 through 91 No H-bonds generated for 'chain 'r' and resid 89 through 91' Processing helix chain 's' and resid 4 through 10 removed outlier: 3.844A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 27 Processing helix chain 's' and resid 40 through 51 Processing helix chain 't' and resid 67 through 69 No H-bonds generated for 'chain 't' and resid 67 through 69' Processing helix chain 'u' and resid 14 through 23 Processing helix chain 'u' and resid 44 through 50 Processing helix chain 'u' and resid 54 through 57 removed outlier: 3.523A pdb=" N TYR u 57 " --> pdb=" O ALA u 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 54 through 57' Processing helix chain 'w' and resid 41 through 43 No H-bonds generated for 'chain 'w' and resid 41 through 43' Processing helix chain 'w' and resid 53 through 62 Processing helix chain 'w' and resid 64 through 74 Processing helix chain 'x' and resid 3 through 7 Processing helix chain 'x' and resid 11 through 33 Processing helix chain 'x' and resid 40 through 61 Processing helix chain 'y' and resid 18 through 27 Processing helix chain 'y' and resid 42 through 50 Processing helix chain 'y' and resid 52 through 54 No H-bonds generated for 'chain 'y' and resid 52 through 54' Processing helix chain 'z' and resid 10 through 19 removed outlier: 4.868A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 20 through 25 Processing sheet with id= B, first strand: chain '2' and resid 14 through 16 Processing sheet with id= C, first strand: chain '3' and resid 2 through 4 Processing sheet with id= D, first strand: chain '3' and resid 14 through 19 Processing sheet with id= E, first strand: chain '4' and resid 10 through 15 Processing sheet with id= F, first strand: chain 'c' and resid 3 through 5 Processing sheet with id= G, first strand: chain 'c' and resid 34 through 36 Processing sheet with id= H, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.245A pdb=" N LEU c 95 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL c 78 " --> pdb=" O LEU c 95 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'c' and resid 129 through 131 Processing sheet with id= J, first strand: chain 'c' and resid 181 through 185 removed outlier: 6.513A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'd' and resid 169 through 172 removed outlier: 4.596A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET d 11 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL d 24 " --> pdb=" O MET d 11 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG d 13 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE d 22 " --> pdb=" O ARG d 13 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS d 190 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL d 177 " --> pdb=" O LYS d 190 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'd' and resid 79 through 83 removed outlier: 6.275A pdb=" N THR d 51 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL d 34 " --> pdb=" O THR d 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'd' and resid 115 through 119 removed outlier: 5.699A pdb=" N MET d 165 " --> pdb=" O LYS d 116 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE d 118 " --> pdb=" O GLY d 163 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY d 163 " --> pdb=" O PHE d 118 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'e' and resid 2 through 4 Processing sheet with id= O, first strand: chain 'e' and resid 118 through 121 removed outlier: 6.335A pdb=" N VAL e 186 " --> pdb=" O ILE e 119 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL e 121 " --> pdb=" O VAL e 186 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET e 188 " --> pdb=" O VAL e 121 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'f' and resid 86 through 91 removed outlier: 6.854A pdb=" N THR f 157 " --> pdb=" O GLU f 32 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE f 34 " --> pdb=" O THR f 155 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR f 155 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU f 36 " --> pdb=" O ASP f 153 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASP f 153 " --> pdb=" O LEU f 36 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'g' and resid 16 through 20 Processing sheet with id= R, first strand: chain 'g' and resid 161 through 164 Processing sheet with id= S, first strand: chain 'g' and resid 95 through 99 Processing sheet with id= T, first strand: chain 'h' and resid 17 through 20 removed outlier: 3.879A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'i' and resid 15 through 19 removed outlier: 6.526A pdb=" N TYR i 53 " --> pdb=" O TYR i 16 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL i 18 " --> pdb=" O TYR i 53 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE i 55 " --> pdb=" O VAL i 18 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'i' and resid 73 through 77 Processing sheet with id= W, first strand: chain 'j' and resid 7 through 9 removed outlier: 6.627A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL j 24 " --> pdb=" O ILE j 38 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ILE j 38 " --> pdb=" O VAL j 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS j 59 " --> pdb=" O LEU j 87 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA j 83 " --> pdb=" O VAL j 63 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'k' and resid 74 through 78 removed outlier: 6.572A pdb=" N PHE k 107 " --> pdb=" O ALA k 75 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE k 77 " --> pdb=" O PHE k 107 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS k 109 " --> pdb=" O ILE k 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'k' and resid 121 through 123 removed outlier: 6.548A pdb=" N LYS k 141 " --> pdb=" O VAL k 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'l' and resid 128 through 132 removed outlier: 3.562A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA l 35 " --> pdb=" O VAL l 101 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL l 101 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'l' and resid 39 through 42 removed outlier: 6.763A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP l 92 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS l 71 " --> pdb=" O TRP l 92 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'm' and resid 33 through 37 Processing sheet with id= AC, first strand: chain 'n' and resid 91 through 93 removed outlier: 3.516A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'o' and resid 83 through 88 removed outlier: 6.474A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLU o 44 " --> pdb=" O ILE o 64 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE o 64 " --> pdb=" O GLU o 44 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE o 50 " --> pdb=" O ALA o 58 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA o 58 " --> pdb=" O ILE o 50 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'q' and resid 10 through 14 removed outlier: 3.735A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLN q 6 " --> pdb=" O VAL q 38 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL q 38 " --> pdb=" O GLN q 6 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'q' and resid 19 through 23 Processing sheet with id= AG, first strand: chain 'q' and resid 32 through 35 removed outlier: 6.386A pdb=" N GLU q 62 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE q 98 " --> pdb=" O GLU q 62 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'q' and resid 72 through 78 removed outlier: 4.105A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'r' and resid 2 through 7 removed outlier: 6.835A pdb=" N SER r 108 " --> pdb=" O VAL r 71 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL r 71 " --> pdb=" O SER r 108 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'r' and resid 82 through 87 Processing sheet with id= AK, first strand: chain 's' and resid 11 through 14 removed outlier: 6.610A pdb=" N LYS s 33 " --> pdb=" O ARG s 12 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL s 31 " --> pdb=" O PRO s 14 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 's' and resid 67 through 70 Processing sheet with id= AM, first strand: chain 't' and resid 22 through 24 Processing sheet with id= AN, first strand: chain 't' and resid 41 through 46 Processing sheet with id= AO, first strand: chain 't' and resid 83 through 88 Processing sheet with id= AP, first strand: chain 't' and resid 25 through 29 removed outlier: 6.730A pdb=" N ILE t 35 " --> pdb=" O LYS t 26 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL t 28 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS t 33 " --> pdb=" O VAL t 28 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'u' and resid 62 through 65 removed outlier: 7.695A pdb=" N ASN u 5 " --> pdb=" O ASP u 43 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP u 43 " --> pdb=" O ASN u 5 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE u 89 " --> pdb=" O ILE u 29 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N TYR u 31 " --> pdb=" O ILE u 89 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE u 91 " --> pdb=" O TYR u 31 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL u 92 " --> pdb=" O ALA u 74 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA u 74 " --> pdb=" O VAL u 92 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'v' and resid 51 through 53 Processing sheet with id= AS, first strand: chain 'v' and resid 66 through 72 Processing sheet with id= AT, first strand: chain 'w' and resid 13 through 18 Processing sheet with id= AU, first strand: chain 'w' and resid 33 through 40 removed outlier: 3.751A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'y' and resid 35 through 38 830 hydrogen bonds defined for protein. 2265 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2658 hydrogen bonds 4164 hydrogen bond angles 0 basepair planarities 1052 basepair parallelities 1496 stacking parallelities Total time for adding SS restraints: 364.32 Time building geometry restraints manager: 47.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9828 1.32 - 1.45: 43588 1.45 - 1.57: 38493 1.57 - 1.70: 6056 1.70 - 1.82: 151 Bond restraints: 98116 Sorted by residual: bond pdb=" C4 U Y 8 " pdb=" O4 U Y 8 " ideal model delta sigma weight residual 1.232 1.589 -0.357 2.00e-02 2.50e+03 3.18e+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 1.484 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.635 1.336 0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.336 0.299 2.00e-02 2.50e+03 2.23e+02 ... (remaining 98111 not shown) Histogram of bond angle deviations from ideal: 64.86 - 80.96: 1 80.96 - 97.07: 1 97.07 - 113.17: 74885 113.17 - 129.27: 70114 129.27 - 145.38: 2495 Bond angle restraints: 147496 Sorted by residual: angle pdb=" O3' C Y 72 " pdb=" P A Y 73 " pdb=" O5' A Y 73 " ideal model delta sigma weight residual 104.00 64.86 39.14 1.50e+00 4.44e-01 6.81e+02 angle pdb=" P A Y 73 " pdb=" O5' A Y 73 " pdb=" C5' A Y 73 " ideal model delta sigma weight residual 120.90 106.53 14.37 1.50e+00 4.44e-01 9.18e+01 angle pdb=" OP1 A Y 73 " pdb=" P A Y 73 " pdb=" OP2 A Y 73 " ideal model delta sigma weight residual 119.60 145.38 -25.78 3.00e+00 1.11e-01 7.38e+01 angle pdb=" C3* PSU a2605 " pdb=" O3* PSU a2605 " pdb=" P C a2606 " ideal model delta sigma weight residual 120.20 107.86 12.34 1.50e+00 4.44e-01 6.77e+01 angle pdb=" C3' C a2606 " pdb=" O3' C a2606 " pdb=" P G a2607 " ideal model delta sigma weight residual 120.20 108.65 11.55 1.50e+00 4.44e-01 5.93e+01 ... (remaining 147491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 55098 35.96 - 71.92: 6930 71.92 - 107.88: 790 107.88 - 143.84: 10 143.84 - 179.80: 7 Dihedral angle restraints: 62835 sinusoidal: 53846 harmonic: 8989 Sorted by residual: dihedral pdb=" CA ASP g 47 " pdb=" C ASP g 47 " pdb=" N ASN g 48 " pdb=" CA ASN g 48 " ideal model delta harmonic sigma weight residual 180.00 -129.40 -50.60 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA HIS 2 31 " pdb=" C HIS 2 31 " pdb=" N ILE 2 32 " pdb=" CA ILE 2 32 " ideal model delta harmonic sigma weight residual -180.00 -132.26 -47.74 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" O4' U a 846 " pdb=" C1' U a 846 " pdb=" N1 U a 846 " pdb=" C2 U a 846 " ideal model delta sinusoidal sigma weight residual 200.00 55.13 144.87 1 1.50e+01 4.44e-03 7.76e+01 ... (remaining 62832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.409: 18889 0.409 - 0.819: 3 0.819 - 1.228: 0 1.228 - 1.638: 0 1.638 - 2.047: 1 Chirality restraints: 18893 Sorted by residual: chirality pdb=" P A Y 73 " pdb=" OP1 A Y 73 " pdb=" OP2 A Y 73 " pdb=" O5' A Y 73 " both_signs ideal model delta sigma weight residual True 2.41 -0.36 2.05 2.00e-01 2.50e+01 1.05e+02 chirality pdb=" C1* PSU a2580 " pdb=" O4* PSU a2580 " pdb=" C2* PSU a2580 " pdb=" C5 PSU a2580 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" P C a 791 " pdb=" OP1 C a 791 " pdb=" OP2 C a 791 " pdb=" O5' C a 791 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.80e+00 ... (remaining 18890 not shown) Planarity restraints: 7377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " -0.076 2.00e-02 2.50e+03 6.05e-01 8.25e+03 pdb=" C4' OMC a2498 " -0.432 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " -0.627 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " 0.610 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " 0.656 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " 0.173 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " -0.998 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " -0.221 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " 0.914 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG a2251 " -0.039 2.00e-02 2.50e+03 5.82e-01 7.62e+03 pdb=" C4' OMG a2251 " -0.445 2.00e-02 2.50e+03 pdb=" O4' OMG a2251 " -0.660 2.00e-02 2.50e+03 pdb=" C3' OMG a2251 " 0.601 2.00e-02 2.50e+03 pdb=" O3' OMG a2251 " 0.584 2.00e-02 2.50e+03 pdb=" C2' OMG a2251 " 0.216 2.00e-02 2.50e+03 pdb=" O2' OMG a2251 " -0.918 2.00e-02 2.50e+03 pdb=" C1' OMG a2251 " -0.220 2.00e-02 2.50e+03 pdb=" N9 OMG a2251 " 0.880 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1962 " 0.852 2.00e-02 2.50e+03 5.69e-01 7.27e+03 pdb=" C4' 5MC a1962 " -0.224 2.00e-02 2.50e+03 pdb=" O4' 5MC a1962 " -0.683 2.00e-02 2.50e+03 pdb=" C3' 5MC a1962 " 0.227 2.00e-02 2.50e+03 pdb=" O3' 5MC a1962 " -0.868 2.00e-02 2.50e+03 pdb=" C2' 5MC a1962 " 0.591 2.00e-02 2.50e+03 pdb=" O2' 5MC a1962 " 0.556 2.00e-02 2.50e+03 pdb=" C1' 5MC a1962 " -0.452 2.00e-02 2.50e+03 pdb=" N1 5MC a1962 " -0.000 2.00e-02 2.50e+03 ... (remaining 7374 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.18: 560 2.18 - 2.92: 39843 2.92 - 3.66: 207029 3.66 - 4.40: 364817 4.40 - 5.14: 489477 Nonbonded interactions: 1101726 Sorted by model distance: nonbonded pdb="MG MG a6235 " pdb=" O HOH a8407 " model vdw 1.446 2.170 nonbonded pdb="MG MG a6232 " pdb=" O HOH a7239 " model vdw 1.530 2.170 nonbonded pdb="MG MG a6232 " pdb=" O HOH a8338 " model vdw 1.689 2.170 nonbonded pdb=" OP2 G a2588 " pdb="MG MG a6061 " model vdw 1.766 2.170 nonbonded pdb="MG MG a6148 " pdb=" O HOH a6508 " model vdw 1.776 2.170 ... (remaining 1101721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 24.520 Check model and map are aligned: 1.220 Set scattering table: 0.650 Process input model: 569.990 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:15.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 622.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 : 0.007 0.357 98116 Z= 0.431 Angle : 0.865 39.140 147496 Z= 0.447 Chirality : 0.047 2.047 18893 Planarity : 0.019 0.605 7377 Dihedral : 23.235 179.801 57047 Min Nonbonded Distance : 1.446 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.47 % Favored : 96.33 % Rotamer: Outliers : 3.72 % Allowed : 13.23 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3108 helix: -1.03 (0.15), residues: 845 sheet: -0.92 (0.18), residues: 642 loop : -1.04 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP c 248 HIS 0.011 0.002 HIS k 35 PHE 0.024 0.003 PHE u 26 TYR 0.023 0.003 TYR p 32 ARG 0.012 0.001 ARG i 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 569 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 29 THR cc_start: 0.7356 (OUTLIER) cc_final: 0.7125 (p) REVERT: 0 37 LYS cc_start: 0.7863 (mttp) cc_final: 0.7571 (ttmt) REVERT: 0 44 ARG cc_start: 0.8230 (mtp180) cc_final: 0.8029 (mtm110) REVERT: c 5 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7170 (mmtt) REVERT: c 21 ASN cc_start: 0.7824 (t0) cc_final: 0.7590 (t0) REVERT: d 58 ASN cc_start: 0.6278 (OUTLIER) cc_final: 0.6029 (m-40) REVERT: e 138 LEU cc_start: 0.8179 (mt) cc_final: 0.7974 (mt) REVERT: e 199 MET cc_start: 0.6426 (ttp) cc_final: 0.5655 (ptp) REVERT: f 21 ASN cc_start: 0.5219 (OUTLIER) cc_final: 0.4933 (m-40) REVERT: f 32 GLU cc_start: 0.5624 (OUTLIER) cc_final: 0.5352 (pp20) REVERT: f 57 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.6030 (mt) REVERT: f 96 MET cc_start: 0.7356 (ttp) cc_final: 0.7100 (ttt) REVERT: f 112 ARG cc_start: 0.4871 (ttm-80) cc_final: 0.4562 (mmt180) REVERT: f 135 GLN cc_start: 0.5199 (OUTLIER) cc_final: 0.4717 (pt0) REVERT: g 29 LYS cc_start: 0.4989 (OUTLIER) cc_final: 0.4680 (pttp) REVERT: m 110 MET cc_start: 0.8806 (mmm) cc_final: 0.8359 (mmm) REVERT: q 31 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6879 (mm-30) REVERT: t 9 ASP cc_start: 0.7593 (m-30) cc_final: 0.7352 (m-30) REVERT: t 102 THR cc_start: 0.7962 (m) cc_final: 0.7596 (t) outliers start: 96 outliers final: 51 residues processed: 638 average time/residue: 2.2413 time to fit residues: 1858.9285 Evaluate side-chains 553 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 494 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 8 LYS Chi-restraints excluded: chain 4 residue 26 SER Chi-restraints excluded: chain 4 residue 47 LYS Chi-restraints excluded: chain 4 residue 48 GLN Chi-restraints excluded: chain 4 residue 65 ASN Chi-restraints excluded: chain c residue 5 LYS Chi-restraints excluded: chain c residue 125 LYS Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain c residue 259 SER Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 123 LYS Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 57 LEU Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 161 LYS Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 LYS Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 58 LYS Chi-restraints excluded: chain m residue 96 ARG Chi-restraints excluded: chain n residue 25 ARG Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 25 GLU Chi-restraints excluded: chain t residue 31 SER Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 511 optimal weight: 6.9990 chunk 459 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 474 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 353 optimal weight: 6.9990 chunk 550 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 36 GLN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 GLN i 128 ASN j 88 ASN m 18 GLN p 20 GLN p 81 ASN q 86 GLN s 28 ASN u 75 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 98116 Z= 0.291 Angle : 0.810 17.344 147496 Z= 0.423 Chirality : 0.043 0.435 18893 Planarity : 0.007 0.146 7377 Dihedral : 23.449 179.935 50948 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.27 % Rotamer: Outliers : 3.65 % Allowed : 15.75 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3108 helix: 0.04 (0.17), residues: 849 sheet: -0.56 (0.18), residues: 655 loop : -0.56 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 248 HIS 0.012 0.002 HIS k 35 PHE 0.024 0.003 PHE u 26 TYR 0.021 0.003 TYR p 32 ARG 0.008 0.001 ARG 2 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 499 time to evaluate : 4.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.7920 (mttp) cc_final: 0.7687 (mttt) REVERT: 0 44 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7942 (mtm110) REVERT: 4 11 GLU cc_start: 0.4034 (OUTLIER) cc_final: 0.3501 (mp0) REVERT: d 58 ASN cc_start: 0.6293 (OUTLIER) cc_final: 0.6046 (m-40) REVERT: e 199 MET cc_start: 0.6404 (ttp) cc_final: 0.5597 (ptp) REVERT: f 3 LYS cc_start: 0.4968 (OUTLIER) cc_final: 0.4573 (tptt) REVERT: f 32 GLU cc_start: 0.5675 (OUTLIER) cc_final: 0.5278 (pp20) REVERT: f 57 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6148 (mt) REVERT: f 112 ARG cc_start: 0.4873 (ttm-80) cc_final: 0.4560 (mmt180) REVERT: f 135 GLN cc_start: 0.5154 (OUTLIER) cc_final: 0.4744 (pt0) REVERT: h 12 LEU cc_start: 0.5633 (OUTLIER) cc_final: 0.5282 (mt) REVERT: i 98 GLU cc_start: 0.8106 (mp0) cc_final: 0.7892 (mp0) REVERT: j 51 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7202 (mtpt) REVERT: m 110 MET cc_start: 0.8838 (mmm) cc_final: 0.8427 (mmm) REVERT: n 17 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7850 (tmtm) REVERT: n 76 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7152 (tttp) REVERT: q 31 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6892 (mm-30) REVERT: t 102 THR cc_start: 0.7950 (m) cc_final: 0.7590 (t) REVERT: u 86 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7902 (mt) outliers start: 94 outliers final: 46 residues processed: 560 average time/residue: 2.2985 time to fit residues: 1680.7419 Evaluate side-chains 537 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 480 time to evaluate : 4.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 4 residue 47 LYS Chi-restraints excluded: chain 4 residue 48 GLN Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain 4 residue 65 ASN Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 125 LYS Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 123 LYS Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 57 LEU Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain j residue 51 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 58 LYS Chi-restraints excluded: chain n residue 17 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 76 LYS Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 25 GLU Chi-restraints excluded: chain t residue 31 SER Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 305 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 458 optimal weight: 1.9990 chunk 374 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 551 optimal weight: 7.9990 chunk 595 optimal weight: 4.9990 chunk 490 optimal weight: 0.7980 chunk 546 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 442 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 GLN i 128 ASN j 88 ASN m 18 GLN q 86 GLN s 28 ASN u 24 ASN u 75 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 98116 Z= 0.264 Angle : 0.769 15.722 147496 Z= 0.404 Chirality : 0.041 0.428 18893 Planarity : 0.007 0.143 7377 Dihedral : 23.388 178.991 50906 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.73 % Favored : 96.17 % Rotamer: Outliers : 4.23 % Allowed : 15.44 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3108 helix: 0.47 (0.17), residues: 843 sheet: -0.39 (0.19), residues: 650 loop : -0.37 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 248 HIS 0.012 0.002 HIS k 35 PHE 0.024 0.002 PHE u 26 TYR 0.020 0.002 TYR p 32 ARG 0.007 0.001 ARG 2 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 485 time to evaluate : 4.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.7972 (mttp) cc_final: 0.7735 (mttt) REVERT: 0 44 ARG cc_start: 0.8201 (mtp180) cc_final: 0.7918 (mtm110) REVERT: 4 4 ASP cc_start: 0.4618 (OUTLIER) cc_final: 0.4263 (t0) REVERT: 4 11 GLU cc_start: 0.3983 (OUTLIER) cc_final: 0.3480 (mp0) REVERT: c 23 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6196 (mt-10) REVERT: d 58 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.6023 (m-40) REVERT: e 162 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7747 (ttp-170) REVERT: e 199 MET cc_start: 0.6356 (ttp) cc_final: 0.5535 (ptp) REVERT: f 3 LYS cc_start: 0.4899 (OUTLIER) cc_final: 0.4577 (tptt) REVERT: f 85 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6417 (pt) REVERT: f 112 ARG cc_start: 0.4905 (ttm-80) cc_final: 0.4582 (mmt180) REVERT: f 135 GLN cc_start: 0.5080 (OUTLIER) cc_final: 0.4683 (pt0) REVERT: j 51 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7034 (mtpt) REVERT: l 6 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6299 (ttp80) REVERT: m 110 MET cc_start: 0.8836 (mmm) cc_final: 0.8414 (mmm) REVERT: n 17 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7862 (tmtm) REVERT: q 21 ARG cc_start: 0.8631 (ttm170) cc_final: 0.8375 (ttm170) REVERT: q 37 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6809 (mt-10) REVERT: t 102 THR cc_start: 0.7961 (m) cc_final: 0.7608 (t) REVERT: u 86 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7836 (mt) outliers start: 109 outliers final: 56 residues processed: 558 average time/residue: 2.2343 time to fit residues: 1635.0605 Evaluate side-chains 542 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 475 time to evaluate : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 12 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 47 LYS Chi-restraints excluded: chain 4 residue 48 GLN Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain 4 residue 65 ASN Chi-restraints excluded: chain 4 residue 66 ILE Chi-restraints excluded: chain c residue 23 GLU Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 125 LYS Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 123 LYS Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 142 ASP Chi-restraints excluded: chain f residue 162 SER Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain j residue 51 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 6 ARG Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain l residue 63 ILE Chi-restraints excluded: chain n residue 17 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 25 GLU Chi-restraints excluded: chain t residue 31 SER Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain y residue 6 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 544 optimal weight: 10.0000 chunk 414 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 370 optimal weight: 10.0000 chunk 553 optimal weight: 9.9990 chunk 585 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 524 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 GLN g 73 ASN g 139 GLN i 128 ASN j 88 ASN m 18 GLN n 38 GLN r 31 GLN s 28 ASN u 24 ASN u 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 98116 Z= 0.532 Angle : 1.096 24.144 147496 Z= 0.541 Chirality : 0.055 0.453 18893 Planarity : 0.010 0.169 7377 Dihedral : 23.521 178.411 50895 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 4.62 % Allowed : 15.05 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3108 helix: 0.01 (0.17), residues: 840 sheet: -0.55 (0.18), residues: 656 loop : -0.55 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP c 248 HIS 0.019 0.003 HIS k 35 PHE 0.030 0.004 PHE u 26 TYR 0.024 0.004 TYR p 32 ARG 0.015 0.002 ARG d 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 494 time to evaluate : 4.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.8085 (mttp) cc_final: 0.7799 (mttt) REVERT: c 23 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6230 (mt-10) REVERT: e 199 MET cc_start: 0.6542 (ttp) cc_final: 0.6277 (ttt) REVERT: f 3 LYS cc_start: 0.4947 (OUTLIER) cc_final: 0.4640 (tptt) REVERT: f 112 ARG cc_start: 0.4972 (ttm-80) cc_final: 0.4544 (mmt180) REVERT: j 51 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7197 (mtpt) REVERT: m 110 MET cc_start: 0.8836 (mmm) cc_final: 0.8460 (mmm) REVERT: n 17 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7970 (tmtm) REVERT: n 76 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7272 (tttp) REVERT: t 102 THR cc_start: 0.8005 (m) cc_final: 0.7635 (t) REVERT: u 86 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7889 (mt) REVERT: w 74 ARG cc_start: 0.6635 (mtm-85) cc_final: 0.6400 (ttm170) outliers start: 119 outliers final: 78 residues processed: 575 average time/residue: 2.2048 time to fit residues: 1662.7777 Evaluate side-chains 575 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 491 time to evaluate : 3.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 3 LYS Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 12 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 40 CYS Chi-restraints excluded: chain 4 residue 47 LYS Chi-restraints excluded: chain 4 residue 48 GLN Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain 4 residue 65 ASN Chi-restraints excluded: chain c residue 23 GLU Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 125 LYS Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 123 LYS Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 194 LYS Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 161 LYS Chi-restraints excluded: chain f residue 162 SER Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 67 THR Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain j residue 51 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain n residue 17 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 63 LYS Chi-restraints excluded: chain n residue 76 LYS Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 34 GLU Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 95 ASP Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 25 GLU Chi-restraints excluded: chain s residue 49 LYS Chi-restraints excluded: chain t residue 31 SER Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain x residue 6 LEU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 487 optimal weight: 6.9990 chunk 332 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 436 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 499 optimal weight: 2.9990 chunk 404 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 299 optimal weight: 10.0000 chunk 525 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 20 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 GLN g 139 GLN i 128 ASN j 88 ASN m 18 GLN r 31 GLN s 28 ASN u 24 ASN u 75 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 98116 Z= 0.252 Angle : 0.761 15.485 147496 Z= 0.402 Chirality : 0.041 0.422 18893 Planarity : 0.007 0.142 7377 Dihedral : 23.387 178.262 50889 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.46 % Rotamer: Outliers : 4.03 % Allowed : 15.32 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3108 helix: 0.44 (0.17), residues: 848 sheet: -0.41 (0.18), residues: 651 loop : -0.33 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 248 HIS 0.012 0.002 HIS k 35 PHE 0.026 0.002 PHE u 26 TYR 0.020 0.002 TYR p 32 ARG 0.006 0.001 ARG d 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 494 time to evaluate : 4.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.7976 (mttp) cc_final: 0.7679 (ttmt) REVERT: 4 4 ASP cc_start: 0.4542 (OUTLIER) cc_final: 0.4206 (t0) REVERT: 4 11 GLU cc_start: 0.3981 (OUTLIER) cc_final: 0.3475 (mp0) REVERT: d 58 ASN cc_start: 0.6313 (OUTLIER) cc_final: 0.6058 (m-40) REVERT: e 199 MET cc_start: 0.6374 (ttp) cc_final: 0.6170 (ttt) REVERT: f 3 LYS cc_start: 0.4993 (OUTLIER) cc_final: 0.4701 (tptt) REVERT: f 112 ARG cc_start: 0.4875 (OUTLIER) cc_final: 0.4567 (mmt180) REVERT: g 27 LYS cc_start: 0.5252 (OUTLIER) cc_final: 0.4986 (tppp) REVERT: g 105 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7542 (mt) REVERT: h 7 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5822 (m-30) REVERT: j 51 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7201 (mtpt) REVERT: m 110 MET cc_start: 0.8818 (mmm) cc_final: 0.8394 (mmm) REVERT: n 17 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7847 (tmtm) REVERT: n 76 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7266 (tttp) REVERT: q 21 ARG cc_start: 0.8633 (ttm170) cc_final: 0.8365 (ttm170) REVERT: q 37 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6828 (mt-10) REVERT: t 102 THR cc_start: 0.7961 (m) cc_final: 0.7604 (t) REVERT: u 86 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7849 (mt) outliers start: 104 outliers final: 66 residues processed: 564 average time/residue: 2.2418 time to fit residues: 1649.6183 Evaluate side-chains 557 residues out of total 2579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 479 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 32 ILE Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 11 GLU Chi-restraints excluded: chain 4 residue 12 ILE Chi-restraints excluded: chain 4 residue 21 VAL Chi-restraints excluded: chain 4 residue 26 SER Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 47 LYS Chi-restraints excluded: chain 4 residue 48 GLN Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain 4 residue 65 ASN Chi-restraints excluded: chain 4 residue 66 ILE Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 125 LYS Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 58 ASN Chi-restraints excluded: chain d residue 62 LYS Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 123 LYS Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 139 LYS Chi-restraints excluded: chain e residue 194 LYS Chi-restraints excluded: chain f residue 3 LYS Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 112 ARG Chi-restraints excluded: chain f residue 129 SER Chi-restraints excluded: chain f residue 162 SER Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 27 LYS Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 56 ASP Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 122 THR Chi-restraints excluded: chain g residue 127 THR Chi-restraints excluded: chain g residue 166 ASP Chi-restraints excluded: chain h residue 7 ASP Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 11 VAL Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain i residue 95 ARG Chi-restraints excluded: chain j residue 51 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain k residue 120 VAL Chi-restraints excluded: chain l residue 14 LYS Chi-restraints excluded: chain n residue 17 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 74 VAL Chi-restraints excluded: chain n residue 76 LYS Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 47 VAL Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 59 GLU Chi-restraints excluded: chain r residue 66 ILE Chi-restraints excluded: chain s residue 25 GLU Chi-restraints excluded: chain t residue 31 SER Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain t residue 100 SER Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 86 LEU Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain x residue 5 GLU Chi-restraints excluded: chain x residue 56 LEU Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain y residue 6 LYS Chi-restraints excluded: chain z residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 197 optimal weight: 10.0000 chunk 527 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 343 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 586 optimal weight: 4.9990 chunk 486 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: