Starting phenix.real_space_refine on Fri Dec 15 17:31:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6x_29787/12_2023/8g6x_29787_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6x_29787/12_2023/8g6x_29787.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6x_29787/12_2023/8g6x_29787_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6x_29787/12_2023/8g6x_29787_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6x_29787/12_2023/8g6x_29787_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6x_29787/12_2023/8g6x_29787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6x_29787/12_2023/8g6x_29787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6x_29787/12_2023/8g6x_29787_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6x_29787/12_2023/8g6x_29787_updated.pdb" } resolution = 2.31 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 7 8.98 5 Zn 2 6.06 5 P 3036 5.49 5 Mg 223 5.21 5 S 82 5.16 5 C 44765 2.51 5 N 16838 2.21 5 O 28920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 ARG 83": "NH1" <-> "NH2" Residue "d GLU 86": "OE1" <-> "OE2" Residue "d ARG 128": "NH1" <-> "NH2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "e GLU 2": "OE1" <-> "OE2" Residue "e TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 144": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "e GLU 197": "OE1" <-> "OE2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" 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 "f GLU 165": "OE1" <-> "OE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" 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 "i GLU 129": "OE1" <-> "OE2" Residue "k GLU 10": "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 "k GLU 143": "OE1" <-> "OE2" 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 "l PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 96": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n GLU 20": "OE1" <-> "OE2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n GLU 84": "OE1" <-> "OE2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" 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 31": "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 54": "OE1" <-> "OE2" Residue "s ARG 73": "NH1" <-> "NH2" Residue "t ARG 6": "NH1" <-> "NH2" Residue "t ARG 7": "NH1" <-> "NH2" Residue "t ARG 82": "NH1" <-> "NH2" Residue "t ARG 86": "NH1" <-> "NH2" Residue "t ARG 94": "NH1" <-> "NH2" Residue "u GLU 55": "OE1" <-> "OE2" Residue "u GLU 69": "OE1" <-> "OE2" Residue "u ASP 76": "OD1" <-> "OD2" Residue "v GLU 17": "OE1" <-> "OE2" Residue "w ARG 3": "NH1" <-> "NH2" Residue "w ARG 11": "NH1" <-> "NH2" Residue "w ARG 37": "NH1" <-> "NH2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w ARG 57": "NH1" <-> "NH2" Residue "w ARG 74": "NH1" <-> "NH2" Residue "x GLU 5": "OE1" <-> "OE2" Residue "x GLU 8": "OE1" <-> "OE2" Residue "x GLU 12": "OE1" <-> "OE2" Residue "x GLU 13": "OE1" <-> "OE2" Residue "x GLU 17": "OE1" <-> "OE2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x ARG 52": "NH1" <-> "NH2" Residue "y ARG 11": "NH1" <-> "NH2" Residue "y ARG 30": "NH1" <-> "NH2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ARG 52": "NH1" <-> "NH2" 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" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 93873 Number of models: 1 Model: "" Number of chains: 72 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: 15 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: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: "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: "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: "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: "a" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 410 Unusual residues: {' K': 5, ' MG': 211, 'SPD': 17, 'SPM': 1} Classifications: {'peptide': 1, 'undetermined': 234} Link IDs: {None: 234} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 21 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1, '3AB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "B" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1, '3AB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' MG': 1, '8AN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3013, 3013 Classifications: {'water': 3013} Link IDs: {None: 3012} Chain: "b" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "c" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "d" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "e" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "l" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "m" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "o" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "p" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "q" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "v" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} 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: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "1" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "2" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 85750 SG CYS 3 11 154.701 86.981 165.133 1.00 14.67 S ATOM 85775 SG CYS 3 14 152.691 84.636 162.745 1.00 16.03 S ATOM 85878 SG CYS 3 27 151.759 85.025 166.438 1.00 16.25 S ATOM 86097 SG CYS 4 16 208.831 152.581 92.583 1.00 46.69 S ATOM 86109 SG CYS 4 18 212.262 152.014 94.579 1.00 50.52 S ATOM 86251 SG CYS 4 37 209.340 149.529 94.135 1.00 46.47 S ATOM 86272 SG CYS 4 40 208.987 152.473 96.495 1.00 51.19 S Time building chain proxies: 38.97, per 1000 atoms: 0.42 Number of scatterers: 93873 At special positions: 0 Unit cell: (230.137, 202.35, 207.337, 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 7 19.00 S 82 16.00 P 3036 15.00 Mg 223 11.99 O 28920 8.00 N 16838 7.00 C 44765 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 45.83 Conformation dependent library (CDL) restraints added in 3.9 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 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " Number of angles added : 9 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 46 sheets defined 26.0% alpha, 19.5% beta 1049 base pairs and 1491 stacking pairs defined. Time for finding SS restraints: 49.98 Creating SS restraints... Processing helix chain 'c' and resid 11 through 14 No H-bonds generated for 'chain 'c' and resid 11 through 14' 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: 3.883A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 208 through 214 removed outlier: 3.556A 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 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 114 Processing helix chain 'e' and resid 131 through 141 Processing helix chain 'e' and resid 156 through 161 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 200 Processing helix chain 'f' and resid 3 through 19 removed outlier: 4.987A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 27 No H-bonds generated for 'chain 'f' and resid 25 through 27' Processing helix chain 'f' and resid 49 through 61 removed outlier: 3.655A pdb=" N ALA f 55 " --> pdb=" O ASP f 51 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP f 56 " --> pdb=" O ASN f 52 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 105 removed outlier: 3.659A pdb=" N TRP f 97 " --> pdb=" O GLY f 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 107 through 110 No H-bonds generated for 'chain 'f' and resid 107 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: 4.081A 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 149 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 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 95 Processing helix chain 'i' and resid 97 through 108 removed outlier: 3.555A pdb=" N GLY i 107 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 121 removed outlier: 3.856A 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 113 through 118 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 83 removed outlier: 4.234A 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 57 Processing helix chain 'l' and resid 110 through 123 removed outlier: 4.125A 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 55 removed outlier: 4.153A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.787A 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: 5.009A 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: 4.355A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.179A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 68 through 85 removed outlier: 3.548A pdb=" N GLU n 84 " --> pdb=" O GLU n 80 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 113 Processing helix chain 'o' and resid 3 through 10 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: 3.795A 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: 3.667A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 85 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: 3.746A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.942A 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 's' and resid 4 through 9 removed outlier: 3.762A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 26 Processing helix chain 's' and resid 40 through 50 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 22 Processing helix chain 'u' and resid 44 through 50 Processing helix chain 'u' and resid 54 through 57 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 34 Processing helix chain 'x' and resid 40 through 60 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: 4.873A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing helix chain '1' and resid 9 through 16 Processing helix chain '1' and resid 18 through 23 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: 4.328A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.079A 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 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 sheet with id= A, first strand: chain 'c' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'c' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'c' and resid 101 through 105 removed outlier: 3.621A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU c 95 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL c 78 " --> pdb=" O LEU c 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'c' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'c' and resid 181 through 185 removed outlier: 6.739A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'd' and resid 169 through 172 removed outlier: 4.653A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET d 11 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL d 24 " --> pdb=" O MET d 11 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG d 13 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE d 22 " --> pdb=" O ARG d 13 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS d 190 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL d 177 " --> pdb=" O LYS d 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'd' and resid 80 through 83 removed outlier: 6.479A pdb=" N THR d 51 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL d 34 " --> pdb=" O THR d 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'd' and resid 115 through 119 removed outlier: 5.873A pdb=" N MET d 165 " --> pdb=" O LYS d 116 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE d 118 " --> pdb=" O GLY d 163 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY d 163 " --> pdb=" O PHE d 118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'e' and resid 2 through 4 Processing sheet with id= J, first strand: chain 'e' and resid 118 through 121 removed outlier: 6.485A pdb=" N VAL e 186 " --> pdb=" O ILE e 119 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL e 121 " --> pdb=" O VAL e 186 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET e 188 " --> pdb=" O VAL e 121 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'f' and resid 128 through 132 removed outlier: 6.918A pdb=" N THR f 68 " --> pdb=" O ILE f 85 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS f 87 " --> pdb=" O LEU f 66 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU f 66 " --> pdb=" O CYS f 87 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'g' and resid 16 through 20 removed outlier: 3.841A pdb=" N LEU g 33 " --> pdb=" O ILE g 26 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'g' and resid 161 through 164 Processing sheet with id= N, first strand: chain 'g' and resid 95 through 99 Processing sheet with id= O, first strand: chain 'h' and resid 18 through 20 Processing sheet with id= P, first strand: chain 'i' and resid 15 through 19 removed outlier: 6.540A pdb=" N TYR i 53 " --> pdb=" O TYR i 16 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL i 18 " --> pdb=" O TYR i 53 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE i 55 " --> pdb=" O VAL i 18 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'i' and resid 73 through 77 Processing sheet with id= R, first strand: chain 'j' and resid 7 through 9 removed outlier: 6.442A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL j 24 " --> pdb=" O ILE j 38 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE j 38 " --> pdb=" O VAL j 24 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA j 83 " --> pdb=" O VAL j 63 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'k' and resid 74 through 78 removed outlier: 6.530A pdb=" N PHE k 107 " --> pdb=" O ALA k 75 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE k 77 " --> pdb=" O PHE k 107 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS k 109 " --> pdb=" O ILE k 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'l' and resid 128 through 132 removed outlier: 3.768A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA l 35 " --> pdb=" O VAL l 101 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL l 101 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'l' and resid 39 through 42 removed outlier: 7.016A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TRP l 92 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS l 71 " --> pdb=" O TRP l 92 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'm' and resid 33 through 37 Processing sheet with id= W, first strand: chain 'n' and resid 91 through 93 removed outlier: 3.530A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'o' and resid 83 through 88 removed outlier: 6.546A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS o 37 " --> pdb=" O GLU o 34 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLU o 44 " --> pdb=" O ILE o 64 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE o 64 " --> pdb=" O GLU o 44 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE o 50 " --> pdb=" O ALA o 58 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA o 58 " --> pdb=" O ILE o 50 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'q' and resid 10 through 15 removed outlier: 3.644A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLN q 6 " --> pdb=" O VAL q 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL q 38 " --> pdb=" O GLN q 6 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'q' and resid 19 through 23 removed outlier: 3.578A pdb=" N ALA q 65 " --> pdb=" O ASP q 95 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'q' and resid 32 through 35 removed outlier: 6.508A pdb=" N GLU q 62 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE q 98 " --> pdb=" O GLU q 62 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'q' and resid 72 through 78 removed outlier: 4.144A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'r' and resid 3 through 7 removed outlier: 6.723A pdb=" N SER r 108 " --> pdb=" O VAL r 71 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL r 71 " --> pdb=" O SER r 108 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'r' and resid 82 through 87 Processing sheet with id= AE, first strand: chain 's' and resid 11 through 14 removed outlier: 6.723A pdb=" N LYS s 33 " --> pdb=" O ARG s 12 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL s 31 " --> pdb=" O PRO s 14 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL s 57 " --> pdb=" O THR s 86 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 's' and resid 67 through 69 Processing sheet with id= AG, first strand: chain 't' and resid 22 through 24 Processing sheet with id= AH, first strand: chain 't' and resid 41 through 45 Processing sheet with id= AI, first strand: chain 't' and resid 83 through 88 removed outlier: 3.578A pdb=" N LYS t 91 " --> pdb=" O GLU t 88 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 't' and resid 25 through 29 removed outlier: 6.638A pdb=" N ILE t 35 " --> pdb=" O LYS t 26 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL t 28 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS t 33 " --> pdb=" O VAL t 28 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'u' and resid 3 through 6 removed outlier: 6.176A pdb=" N THR u 62 " --> pdb=" O ILE u 4 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ALA u 6 " --> pdb=" O THR u 62 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL u 64 " --> pdb=" O ALA u 6 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP u 90 " --> pdb=" O GLN u 75 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL u 77 " --> pdb=" O HIS u 88 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS u 88 " --> pdb=" O VAL u 77 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'v' and resid 51 through 53 Processing sheet with id= AM, first strand: chain 'v' and resid 66 through 72 Processing sheet with id= AN, first strand: chain 'w' and resid 13 through 18 Processing sheet with id= AO, first strand: chain 'w' and resid 33 through 40 removed outlier: 3.522A pdb=" N ARG w 45 " --> pdb=" O VAL w 40 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'y' and resid 35 through 38 Processing sheet with id= AQ, first strand: chain '0' and resid 20 through 23 Processing sheet with id= AR, first strand: chain '3' and resid 2 through 4 Processing sheet with id= AS, first strand: chain '3' and resid 14 through 19 Processing sheet with id= AT, first strand: chain '4' and resid 21 through 26 removed outlier: 5.564A pdb=" N LEU 4 32 " --> pdb=" O SER 4 15 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2653 hydrogen bonds 4158 hydrogen bond angles 0 basepair planarities 1049 basepair parallelities 1491 stacking parallelities Total time for adding SS restraints: 373.09 Time building geometry restraints manager: 48.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.69: 98156 1.69 - 2.19: 145 2.19 - 2.69: 0 2.69 - 3.19: 0 3.19 - 3.69: 1 Bond restraints: 98302 Sorted by residual: bond pdb=" C1' U Y 39 " pdb=" N1 U Y 39 " ideal model delta sigma weight residual 1.480 3.692 -2.212 1.50e-02 4.44e+03 2.17e+04 bond pdb=" C4 U Y 8 " pdb=" O4 U Y 8 " ideal model delta sigma weight residual 1.232 1.591 -0.359 2.00e-02 2.50e+03 3.23e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.479 0.323 2.00e-02 2.50e+03 2.61e+02 bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.489 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.635 1.332 0.303 2.00e-02 2.50e+03 2.30e+02 ... (remaining 98297 not shown) Histogram of bond angle deviations from ideal: 19.41 - 43.29: 1 43.29 - 67.17: 0 67.17 - 91.05: 2 91.05 - 114.93: 82708 114.93 - 138.81: 64959 Bond angle restraints: 147670 Sorted by residual: angle pdb=" C1' U Y 39 " pdb=" N1 U Y 39 " pdb=" C6 U Y 39 " ideal model delta sigma weight residual 121.20 19.41 101.79 3.00e+00 1.11e-01 1.15e+03 angle pdb=" O3' A a2453 " pdb=" P G a2454 " pdb=" O5' G a2454 " ideal model delta sigma weight residual 104.00 75.72 28.28 1.50e+00 4.44e-01 3.56e+02 angle pdb=" O4' U Y 39 " pdb=" C1' U Y 39 " pdb=" N1 U Y 39 " ideal model delta sigma weight residual 108.50 89.75 18.75 1.50e+00 4.44e-01 1.56e+02 angle pdb=" C1' 6MZ a2030 " pdb=" N9 6MZ a2030 " pdb=" C8 6MZ a2030 " ideal model delta sigma weight residual 91.39 128.66 -37.27 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C3' A a2453 " pdb=" O3' A a2453 " pdb=" P G a2454 " ideal model delta sigma weight residual 120.20 138.81 -18.61 1.50e+00 4.44e-01 1.54e+02 ... (remaining 147665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 53650 35.52 - 71.04: 6116 71.04 - 106.56: 870 106.56 - 142.09: 12 142.09 - 177.61: 7 Dihedral angle restraints: 60655 sinusoidal: 51662 harmonic: 8993 Sorted by residual: 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 -126.49 -53.51 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" O4' U a2321 " pdb=" C1' U a2321 " pdb=" N1 U a2321 " pdb=" C2 U a2321 " ideal model delta sinusoidal sigma weight residual 200.00 42.85 157.15 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 59.94 140.06 1 1.50e+01 4.44e-03 7.54e+01 ... (remaining 60652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.843: 18861 0.843 - 1.687: 0 1.687 - 2.530: 0 2.530 - 3.373: 0 3.373 - 4.217: 1 Chirality restraints: 18862 Sorted by residual: chirality pdb=" C1' U Y 39 " pdb=" O4' U Y 39 " pdb=" C2' U Y 39 " pdb=" N1 U Y 39 " both_signs ideal model delta sigma weight residual False 2.47 6.68 -4.22 2.00e-01 2.50e+01 4.44e+02 chirality pdb=" P C Y 72 " pdb=" OP1 C Y 72 " pdb=" OP2 C Y 72 " pdb=" O5' C Y 72 " both_signs ideal model delta sigma weight residual True 2.41 -2.86 -0.45 2.00e-01 2.50e+01 5.00e+00 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 2.13 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 18859 not shown) Planarity restraints: 7389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M a2069 " -0.063 2.00e-02 2.50e+03 6.15e-01 8.50e+03 pdb=" C4' G7M a2069 " -0.451 2.00e-02 2.50e+03 pdb=" O4' G7M a2069 " -0.671 2.00e-02 2.50e+03 pdb=" C3' G7M a2069 " 0.595 2.00e-02 2.50e+03 pdb=" O3' G7M a2069 " 0.653 2.00e-02 2.50e+03 pdb=" C2' G7M a2069 " 0.170 2.00e-02 2.50e+03 pdb=" O2' G7M a2069 " -0.982 2.00e-02 2.50e+03 pdb=" C1' G7M a2069 " -0.214 2.00e-02 2.50e+03 pdb=" N9 G7M a2069 " 0.962 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 6MZ a1618 " 0.905 2.00e-02 2.50e+03 6.09e-01 8.35e+03 pdb=" C4' 6MZ a1618 " -0.207 2.00e-02 2.50e+03 pdb=" O4' 6MZ a1618 " -0.726 2.00e-02 2.50e+03 pdb=" C3' 6MZ a1618 " 0.200 2.00e-02 2.50e+03 pdb=" O3' 6MZ a1618 " -0.954 2.00e-02 2.50e+03 pdb=" C2' 6MZ a1618 " 0.628 2.00e-02 2.50e+03 pdb=" O2' 6MZ a1618 " 0.640 2.00e-02 2.50e+03 pdb=" C1' 6MZ a1618 " -0.444 2.00e-02 2.50e+03 pdb=" N9 6MZ a1618 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG a2251 " -0.036 2.00e-02 2.50e+03 5.80e-01 7.56e+03 pdb=" C4' OMG a2251 " -0.445 2.00e-02 2.50e+03 pdb=" O4' OMG a2251 " -0.689 2.00e-02 2.50e+03 pdb=" C3' OMG a2251 " 0.585 2.00e-02 2.50e+03 pdb=" O3' OMG a2251 " 0.562 2.00e-02 2.50e+03 pdb=" C2' OMG a2251 " 0.226 2.00e-02 2.50e+03 pdb=" O2' OMG a2251 " -0.889 2.00e-02 2.50e+03 pdb=" C1' OMG a2251 " -0.212 2.00e-02 2.50e+03 pdb=" N9 OMG a2251 " 0.898 2.00e-02 2.50e+03 ... (remaining 7386 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.21: 593 2.21 - 2.94: 41849 2.94 - 3.67: 211985 3.67 - 4.41: 362773 4.41 - 5.14: 487181 Nonbonded interactions: 1104381 Sorted by model distance: nonbonded pdb=" C1' U Y 39 " pdb=" C5 U Y 39 " model vdw 1.474 3.016 nonbonded pdb=" OP1 G a2588 " pdb="MG MG a6020 " model vdw 1.615 2.170 nonbonded pdb="MG MG c 303 " pdb=" O HOH a9033 " model vdw 1.665 2.170 nonbonded pdb="MG MG a6030 " pdb=" O HOH a8680 " model vdw 1.795 2.170 nonbonded pdb=" OP2 G a2822 " pdb="MG MG a6110 " model vdw 1.800 2.170 ... (remaining 1104376 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.230 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: 0.090 Extract box with map and model: 28.400 Check model and map are aligned: 1.080 Set scattering table: 0.660 Process input model: 586.980 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.300 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 640.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 2.212 98302 Z= 0.521 Angle : 0.987 101.789 147670 Z= 0.488 Chirality : 0.057 4.217 18862 Planarity : 0.027 0.615 7389 Dihedral : 22.700 177.606 54865 Min Nonbonded Distance : 1.474 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.08 % Favored : 95.76 % Rotamer: Outliers : 5.85 % Allowed : 15.78 % Favored : 78.36 % 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: -2.02 (0.13), residues: 3110 helix: -1.17 (0.15), residues: 840 sheet: -1.24 (0.18), residues: 657 loop : -1.41 (0.13), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP l 64 HIS 0.014 0.002 HIS k 35 PHE 0.023 0.003 PHE m 21 TYR 0.025 0.003 TYR r 38 ARG 0.013 0.001 ARG 0 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 522 time to evaluate : 4.218 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 87 residues processed: 639 average time/residue: 2.1790 time to fit residues: 1834.1977 Evaluate side-chains 527 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 440 time to evaluate : 4.177 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 75 residues processed: 13 average time/residue: 1.1429 time to fit residues: 27.8979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 511 optimal weight: 9.9990 chunk 459 optimal weight: 20.0000 chunk 254 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 309 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 474 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 288 optimal weight: 3.9990 chunk 353 optimal weight: 0.9990 chunk 550 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 37 ASN ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 49 GLN g 22 GLN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN o 3 ASN q 86 GLN t 40 ASN x 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.314 98302 Z= 0.248 Angle : 0.838 90.530 147670 Z= 0.427 Chirality : 0.039 0.385 18862 Planarity : 0.008 0.140 7389 Dihedral : 22.737 179.469 48644 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 6.09 % Allowed : 18.38 % Favored : 75.53 % 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: -0.95 (0.14), residues: 3110 helix: 0.13 (0.17), residues: 829 sheet: -0.80 (0.18), residues: 653 loop : -0.88 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP l 64 HIS 0.009 0.001 HIS k 35 PHE 0.020 0.002 PHE f 122 TYR 0.020 0.002 TYR r 38 ARG 0.007 0.001 ARG c 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 458 time to evaluate : 4.105 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 92 residues processed: 571 average time/residue: 2.1454 time to fit residues: 1617.3532 Evaluate side-chains 524 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 432 time to evaluate : 4.248 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 73 residues processed: 21 average time/residue: 1.0889 time to fit residues: 41.3685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 458 optimal weight: 6.9990 chunk 374 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 551 optimal weight: 9.9990 chunk 595 optimal weight: 20.0000 chunk 490 optimal weight: 6.9990 chunk 546 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 442 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 23 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN o 3 ASN p 56 GLN t 40 ASN x 27 ASN 1 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.234 98302 Z= 0.415 Angle : 1.010 55.028 147670 Z= 0.508 Chirality : 0.048 0.417 18862 Planarity : 0.010 0.155 7389 Dihedral : 22.867 178.751 48644 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.31 % Favored : 95.53 % Rotamer: Outliers : 6.09 % Allowed : 19.08 % Favored : 74.84 % 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: -0.99 (0.14), residues: 3110 helix: 0.03 (0.17), residues: 827 sheet: -0.71 (0.19), residues: 651 loop : -0.94 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP p 61 HIS 0.016 0.002 HIS k 35 PHE 0.042 0.003 PHE f 122 TYR 0.027 0.003 TYR g 157 ARG 0.014 0.001 ARG j 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 433 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 96 residues processed: 551 average time/residue: 2.1491 time to fit residues: 1562.9381 Evaluate side-chains 520 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 424 time to evaluate : 4.180 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 83 residues processed: 14 average time/residue: 1.1862 time to fit residues: 30.4570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 544 optimal weight: 0.9990 chunk 414 optimal weight: 0.7980 chunk 286 optimal weight: 0.1980 chunk 61 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 370 optimal weight: 7.9990 chunk 553 optimal weight: 0.9980 chunk 585 optimal weight: 4.9990 chunk 289 optimal weight: 0.6980 chunk 524 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 90 ASN ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 22 GLN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 116 GLN ** i 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN o 3 ASN p 72 ASN q 86 GLN t 40 ASN w 20 HIS x 27 ASN 1 29 GLN 4 20 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 98302 Z= 0.122 Angle : 0.661 16.593 147670 Z= 0.366 Chirality : 0.035 0.399 18862 Planarity : 0.007 0.130 7389 Dihedral : 22.569 178.786 48644 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 5.31 % Allowed : 19.50 % Favored : 75.18 % 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: -0.32 (0.14), residues: 3110 helix: 0.76 (0.18), residues: 826 sheet: -0.46 (0.19), residues: 643 loop : -0.55 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP l 64 HIS 0.005 0.001 HIS e 165 PHE 0.011 0.001 PHE m 21 TYR 0.015 0.001 TYR r 38 ARG 0.006 0.000 ARG k 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 465 time to evaluate : 4.479 Fit side-chains revert: symmetry clash outliers start: 137 outliers final: 76 residues processed: 573 average time/residue: 2.1698 time to fit residues: 1645.7081 Evaluate side-chains 510 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 434 time to evaluate : 4.260 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 68 residues processed: 9 average time/residue: 1.3693 time to fit residues: 22.8063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 487 optimal weight: 2.9990 chunk 332 optimal weight: 0.0980 chunk 8 optimal weight: 10.0000 chunk 436 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 499 optimal weight: 4.9990 chunk 404 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 299 optimal weight: 0.6980 chunk 525 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN m 18 GLN o 3 ASN x 27 ASN 1 29 GLN 4 20 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 98302 Z= 0.185 Angle : 0.707 17.096 147670 Z= 0.385 Chirality : 0.037 0.396 18862 Planarity : 0.007 0.138 7389 Dihedral : 22.555 176.654 48644 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 4.46 % Allowed : 20.55 % Favored : 74.99 % 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: -0.27 (0.14), residues: 3110 helix: 0.76 (0.18), residues: 831 sheet: -0.42 (0.19), residues: 629 loop : -0.49 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP l 64 HIS 0.007 0.001 HIS k 35 PHE 0.016 0.002 PHE m 21 TYR 0.019 0.002 TYR p 32 ARG 0.007 0.001 ARG d 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 450 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 87 residues processed: 540 average time/residue: 2.1301 time to fit residues: 1522.3603 Evaluate side-chains 523 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 436 time to evaluate : 4.552 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 72 residues processed: 16 average time/residue: 1.4047 time to fit residues: 38.3315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 115 optimal weight: 10.0000 chunk 343 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 586 optimal weight: 20.0000 chunk 486 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 307 optimal weight: 0.9980 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN o 3 ASN ** u 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 27 ASN 1 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 98302 Z= 0.410 Angle : 0.984 20.333 147670 Z= 0.500 Chirality : 0.048 0.422 18862 Planarity : 0.009 0.155 7389 Dihedral : 22.799 177.745 48644 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.31 % Favored : 95.56 % Rotamer: Outliers : 5.04 % Allowed : 20.12 % Favored : 74.84 % 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: -0.71 (0.14), residues: 3110 helix: 0.25 (0.17), residues: 827 sheet: -0.57 (0.19), residues: 659 loop : -0.73 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP w 39 HIS 0.017 0.002 HIS k 35 PHE 0.036 0.003 PHE f 122 TYR 0.027 0.003 TYR p 32 ARG 0.008 0.001 ARG w 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 434 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 90 residues processed: 535 average time/residue: 2.1755 time to fit residues: 1539.3000 Evaluate side-chains 512 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 422 time to evaluate : 4.153 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 78 residues processed: 13 average time/residue: 1.2121 time to fit residues: 29.0088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 565 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 428 optimal weight: 5.9990 chunk 331 optimal weight: 8.9990 chunk 493 optimal weight: 0.7980 chunk 327 optimal weight: 0.9990 chunk 584 optimal weight: 6.9990 chunk 365 optimal weight: 9.9990 chunk 356 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN o 3 ASN o 7 GLN p 72 ASN r 31 GLN ** u 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 20 HIS x 27 ASN 1 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 98302 Z= 0.255 Angle : 0.800 16.936 147670 Z= 0.425 Chirality : 0.041 0.392 18862 Planarity : 0.008 0.145 7389 Dihedral : 22.680 176.843 48644 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 4.96 % Allowed : 20.47 % Favored : 74.56 % 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: -0.54 (0.14), residues: 3110 helix: 0.47 (0.18), residues: 823 sheet: -0.53 (0.19), residues: 644 loop : -0.64 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP w 39 HIS 0.010 0.001 HIS k 35 PHE 0.022 0.002 PHE f 122 TYR 0.021 0.002 TYR p 32 ARG 0.005 0.001 ARG k 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 436 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 91 residues processed: 533 average time/residue: 2.1799 time to fit residues: 1541.1647 Evaluate side-chains 513 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 422 time to evaluate : 4.281 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 76 residues processed: 16 average time/residue: 1.2185 time to fit residues: 34.6818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 606 random chunks: chunk 361 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 348 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 371 optimal weight: 9.9990 chunk 397 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 459 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN o 3 ASN p 72 ASN r 31 GLN u 12 GLN x 27 ASN 1 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 98302 Z= 0.272 Angle : 0.821 16.902 147670 Z= 0.433 Chirality : 0.041 0.400 18862 Planarity : 0.008 0.147 7389 Dihedral : 22.686 176.125 48644 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 4.61 % Allowed : 20.71 % Favored : 74.68 % 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: -0.55 (0.14), residues: 3110 helix: 0.42 (0.17), residues: 825 sheet: -0.53 (0.19), residues: 644 loop : -0.64 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP w 39 HIS 0.011 0.002 HIS k 35 PHE 0.023 0.003 PHE f 122 TYR 0.022 0.003 TYR p 32 ARG 0.009 0.001 ARG k 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6220 Ramachandran restraints generated. 3110 Oldfield, 0 Emsley, 3110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 429 time to evaluate : 4.301 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 91 residues processed: 529 average time/residue: 2.1781 time to fit residues: 1526.2360 Evaluate side-chains 512 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 421 time to evaluate : 4.166 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 81 residues processed: 11 average time/residue: 1.1291 time to fit residues: 24.1760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.9707 > 50: distance: 53 - 58: 28.073 distance: 58 - 59: 19.023 distance: 59 - 60: 45.868 distance: 60 - 61: 23.895 distance: 60 - 62: 22.269 distance: 62 - 63: 23.069 distance: 63 - 64: 28.012 distance: 63 - 66: 22.371 distance: 64 - 65: 4.316 distance: 64 - 71: 13.507 distance: 66 - 67: 19.370 distance: 67 - 68: 18.079 distance: 68 - 69: 4.329 distance: 68 - 70: 11.981 distance: 71 - 72: 10.818 distance: 72 - 73: 39.508 distance: 72 - 75: 40.174 distance: 73 - 74: 18.303 distance: 73 - 78: 15.994 distance: 75 - 76: 27.002 distance: 75 - 77: 5.007 distance: 78 - 79: 23.218 distance: 78 - 201: 22.990 distance: 79 - 80: 10.350 distance: 79 - 82: 21.457 distance: 80 - 81: 13.520 distance: 80 - 85: 26.097 distance: 81 - 198: 28.334 distance: 82 - 83: 31.496 distance: 82 - 84: 39.839 distance: 85 - 86: 18.272 distance: 86 - 87: 15.456 distance: 86 - 89: 8.859 distance: 87 - 88: 18.397 distance: 87 - 94: 17.791 distance: 89 - 90: 13.856 distance: 90 - 91: 8.338 distance: 91 - 92: 3.235 distance: 91 - 93: 3.298 distance: 94 - 95: 12.237 distance: 94 - 185: 18.231 distance: 95 - 96: 10.782 distance: 95 - 98: 8.361 distance: 96 - 97: 29.121 distance: 96 - 105: 33.551 distance: 97 - 182: 36.116 distance: 98 - 99: 12.204 distance: 99 - 100: 6.511 distance: 99 - 101: 10.930 distance: 100 - 102: 7.965 distance: 101 - 103: 5.832 distance: 102 - 104: 12.366 distance: 103 - 104: 8.143 distance: 105 - 106: 20.331 distance: 106 - 107: 4.254 distance: 106 - 109: 20.083 distance: 107 - 108: 4.556 distance: 107 - 110: 31.638 distance: 110 - 111: 14.672 distance: 111 - 112: 5.228 distance: 111 - 114: 3.427 distance: 112 - 113: 5.299 distance: 112 - 119: 14.207 distance: 114 - 115: 12.644 distance: 115 - 116: 7.108 distance: 116 - 117: 14.112 distance: 116 - 118: 9.110 distance: 120 - 121: 7.851 distance: 120 - 123: 10.128 distance: 121 - 122: 9.557 distance: 121 - 126: 10.991 distance: 123 - 124: 15.178 distance: 123 - 125: 15.274 distance: 126 - 127: 14.260 distance: 127 - 128: 13.469 distance: 127 - 130: 13.476 distance: 128 - 134: 28.575 distance: 130 - 131: 13.601 distance: 131 - 132: 16.757 distance: 131 - 133: 13.133