Starting phenix.real_space_refine on Thu Feb 22 06:04:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/02_2024/6s0k_10073_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/02_2024/6s0k_10073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/02_2024/6s0k_10073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/02_2024/6s0k_10073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/02_2024/6s0k_10073_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/02_2024/6s0k_10073_neut.pdb" } resolution = 3.1 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= 0.015 sd= 0.411 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3006 5.49 5 Mg 68 5.21 5 S 119 5.16 5 C 50183 2.51 5 N 18302 2.21 5 O 27029 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 GLU 145": "OE1" <-> "OE2" 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 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "F GLU 19": "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 "G ARG 3": "NH1" <-> "NH2" 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 "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 65": "OE1" <-> "OE2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "L GLU 4": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 104": "OE1" <-> "OE2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 114": "OE1" <-> "OE2" Residue "O GLU 123": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "P GLU 112": "OE1" <-> "OE2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 71": "OE1" <-> "OE2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "S TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 23": "OE1" <-> "OE2" Residue "S GLU 31": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 54": "OE1" <-> "OE2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "X GLU 17": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "c GLU 51": "OE1" <-> "OE2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "h GLU 34": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h ARG 51": "NH1" <-> "NH2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "h GLU 61": "OE1" <-> "OE2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h GLU 101": "OE1" <-> "OE2" Residue "h ARG 103": "NH1" <-> "NH2" Residue "h GLU 148": "OE1" <-> "OE2" Residue "h GLU 196": "OE1" <-> "OE2" Residue "h GLU 230": "OE1" <-> "OE2" Residue "h GLU 250": "OE1" <-> "OE2" Residue "h GLU 260": "OE1" <-> "OE2" Residue "h GLU 267": "OE1" <-> "OE2" Residue "h GLU 296": "OE1" <-> "OE2" Residue "h GLU 332": "OE1" <-> "OE2" Residue "h ARG 382": "NH1" <-> "NH2" Residue "h GLU 431": "OE1" <-> "OE2" Residue "h GLU 463": "OE1" <-> "OE2" Residue "h GLU 468": "OE1" <-> "OE2" Residue "h GLU 487": "OE1" <-> "OE2" Residue "h ARG 509": "NH1" <-> "NH2" Residue "h GLU 522": "OE1" <-> "OE2" Residue "h GLU 535": "OE1" <-> "OE2" Residue "h ARG 566": "NH1" <-> "NH2" Residue "h ARG 574": "NH1" <-> "NH2" Residue "h ARG 585": "NH1" <-> "NH2" Residue "h ARG 596": "NH1" <-> "NH2" Residue "h GLU 619": "OE1" <-> "OE2" Residue "h ARG 637": "NH1" <-> "NH2" Residue "h ARG 642": "NH1" <-> "NH2" Residue "h ARG 657": "NH1" <-> "NH2" Residue "h GLU 699": "OE1" <-> "OE2" Residue "h GLU 708": "OE1" <-> "OE2" Residue "h GLU 727": "OE1" <-> "OE2" Residue "h GLU 729": "OE1" <-> "OE2" Residue "h GLU 733": "OE1" <-> "OE2" Residue "h GLU 737": "OE1" <-> "OE2" Residue "h GLU 745": "OE1" <-> "OE2" Residue "h ARG 749": "NH1" <-> "NH2" Residue "h GLU 752": "OE1" <-> "OE2" Residue "h GLU 802": "OE1" <-> "OE2" Residue "h ARG 832": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 98708 Number of models: 1 Model: "" Number of chains: 39 Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 61902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2883, 61902 Classifications: {'RNA': 2883} Modifications used: {'rna2p_pur': 280, 'rna2p_pyr': 148, 'rna3p_pur': 1386, 'rna3p_pyr': 1069} Link IDs: {'rna2p': 428, 'rna3p': 2454} Chain breaks: 4 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1411 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 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: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 946 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "K" 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: "L" 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: "M" 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: "N" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" 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: "R" 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: "S" 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: "T" 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: "U" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "V" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "X" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" 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: "Z" 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: "a" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "h" Number of atoms: 6672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6672 Classifications: {'peptide': 838} Link IDs: {'PTRANS': 27, 'TRANS': 810} Chain: "k" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 374 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Unusual residues: {' MG': 65} Classifications: {'undetermined': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 91376 SG CYS f 11 79.085 80.901 178.687 1.00 81.75 S ATOM 91401 SG CYS f 14 82.005 82.822 177.118 1.00 82.14 S ATOM 91504 SG CYS f 27 82.074 78.846 179.006 1.00 84.24 S Time building chain proxies: 37.88, per 1000 atoms: 0.38 Number of scatterers: 98708 At special positions: 0 Unit cell: (264.1, 197.38, 241.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 119 16.00 P 3006 15.00 Mg 68 11.99 O 27029 8.00 N 18302 7.00 C 50183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.92 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " Number of angles added : 3 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8048 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 54 sheets defined 36.3% alpha, 19.2% beta 1032 base pairs and 1656 stacking pairs defined. Time for finding SS restraints: 33.65 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.344A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.825A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.626A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 102 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 38 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.933A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 24 through 28 removed outlier: 3.702A pdb=" N GLN F 27 " --> pdb=" O SER F 24 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 28 " --> pdb=" O VAL F 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 28' Processing helix chain 'F' and resid 41 through 45 removed outlier: 4.233A pdb=" N ILE F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 62 removed outlier: 3.977A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.730A pdb=" N MET F 96 " --> pdb=" O ARG F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.725A pdb=" N ILE F 111 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 173 removed outlier: 3.588A pdb=" N GLY F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 81 Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 50 through 74 Processing helix chain 'H' and resid 95 through 103 removed outlier: 3.554A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 22 Processing helix chain 'I' and resid 34 through 49 Processing helix chain 'I' and resid 56 through 65 removed outlier: 3.706A pdb=" N GLU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 75 removed outlier: 4.573A pdb=" N CYS I 71 " --> pdb=" O PRO I 68 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP I 74 " --> pdb=" O CYS I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 104 removed outlier: 3.789A pdb=" N LYS I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN I 103 " --> pdb=" O PHE I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 126 removed outlier: 3.507A pdb=" N GLN I 122 " --> pdb=" O PRO I 119 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE I 123 " --> pdb=" O ALA I 120 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP I 124 " --> pdb=" O SER I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 30 removed outlier: 3.764A pdb=" N GLN J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 46 removed outlier: 4.400A pdb=" N PHE J 38 " --> pdb=" O ASN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 75 through 83 Processing helix chain 'J' and resid 102 through 115 Processing helix chain 'J' and resid 121 through 134 removed outlier: 3.705A pdb=" N MET J 125 " --> pdb=" O ASP J 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.238A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.761A pdb=" N VAL K 62 " --> pdb=" O ALA K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 96 Processing helix chain 'K' and resid 97 through 109 removed outlier: 4.036A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE K 103 " --> pdb=" O ARG K 99 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 Processing helix chain 'K' and resid 132 through 136 Processing helix chain 'L' and resid 104 through 108 removed outlier: 3.717A pdb=" N LEU L 107 " --> pdb=" O THR L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 118 Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.582A pdb=" N ARG M 41 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.689A pdb=" N LEU M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.603A pdb=" N ALA M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 98 Processing helix chain 'M' and resid 128 through 138 removed outlier: 3.528A pdb=" N ALA M 137 " --> pdb=" O ALA M 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 57 removed outlier: 3.779A pdb=" N VAL N 57 " --> pdb=" O MET N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 122 Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 55 removed outlier: 4.447A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 72 through 82 Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 117 through 125 removed outlier: 3.654A pdb=" N LYS O 121 " --> pdb=" O ASP O 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 22 removed outlier: 3.654A pdb=" N ALA P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 60 removed outlier: 3.593A pdb=" N ALA P 59 " --> pdb=" O GLU P 55 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU P 60 " --> pdb=" O LYS P 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 55 through 60' Processing helix chain 'P' and resid 67 through 85 removed outlier: 3.504A pdb=" N ALA P 71 " --> pdb=" O ASN P 67 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS P 85 " --> pdb=" O ARG P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 113 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 53 through 56 removed outlier: 4.172A pdb=" N HIS Q 56 " --> pdb=" O ARG Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 97 through 102 removed outlier: 3.525A pdb=" N LEU Q 100 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU Q 102 " --> pdb=" O TYR Q 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 108 removed outlier: 3.551A pdb=" N ALA Q 107 " --> pdb=" O THR Q 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 21 removed outlier: 3.617A pdb=" N ALA R 10 " --> pdb=" O ARG R 6 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 31 through 70 removed outlier: 3.934A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 73 No H-bonds generated for 'chain 'R' and resid 71 through 73' Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 118 Processing helix chain 'T' and resid 13 through 22 removed outlier: 3.890A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP T 22 " --> pdb=" O ARG T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 38 removed outlier: 3.743A pdb=" N TYR T 38 " --> pdb=" O ASP T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 61 removed outlier: 3.616A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 89 through 91 No H-bonds generated for 'chain 'T' and resid 89 through 91' Processing helix chain 'U' and resid 3 through 8 Processing helix chain 'U' and resid 17 through 28 Processing helix chain 'U' and resid 39 through 51 Processing helix chain 'V' and resid 49 through 53 Processing helix chain 'W' and resid 13 through 23 removed outlier: 3.598A pdb=" N SER W 17 " --> pdb=" O GLY W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 51 Processing helix chain 'W' and resid 53 through 58 Processing helix chain 'Y' and resid 53 through 63 Processing helix chain 'Y' and resid 63 through 75 removed outlier: 3.814A pdb=" N VAL Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 34 Processing helix chain 'Z' and resid 40 through 62 removed outlier: 4.557A pdb=" N LYS Z 44 " --> pdb=" O SER Z 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 27 Processing helix chain 'a' and resid 41 through 51 removed outlier: 3.550A pdb=" N VAL a 51 " --> pdb=" O MET a 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 17 removed outlier: 3.692A pdb=" N ARG b 13 " --> pdb=" O THR b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 20 No H-bonds generated for 'chain 'b' and resid 18 through 20' Processing helix chain 'd' and resid 8 through 17 Processing helix chain 'd' and resid 17 through 22 Processing helix chain 'd' and resid 24 through 37 Processing helix chain 'e' and resid 7 through 13 removed outlier: 3.581A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 45 Processing helix chain 'e' and resid 54 through 62 Processing helix chain 'f' and resid 30 through 33 Processing helix chain 'h' and resid 1 through 29 Processing helix chain 'h' and resid 44 through 56 removed outlier: 4.139A pdb=" N ALA h 48 " --> pdb=" O LYS h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 60 through 62 No H-bonds generated for 'chain 'h' and resid 60 through 62' Processing helix chain 'h' and resid 63 through 78 removed outlier: 4.446A pdb=" N ALA h 69 " --> pdb=" O PRO h 65 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA h 74 " --> pdb=" O VAL h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 96 removed outlier: 3.701A pdb=" N GLU h 96 " --> pdb=" O MET h 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 121 removed outlier: 4.444A pdb=" N LEU h 114 " --> pdb=" O LEU h 110 " (cutoff:3.500A) Proline residue: h 115 - end of helix removed outlier: 3.642A pdb=" N LEU h 121 " --> pdb=" O TYR h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 132 through 149 removed outlier: 3.972A pdb=" N ALA h 136 " --> pdb=" O ASN h 132 " (cutoff:3.500A) Proline residue: h 145 - end of helix Processing helix chain 'h' and resid 162 through 171 Processing helix chain 'h' and resid 179 through 191 Processing helix chain 'h' and resid 194 through 198 removed outlier: 3.547A pdb=" N ARG h 198 " --> pdb=" O PRO h 195 " (cutoff:3.500A) Processing helix chain 'h' and resid 216 through 220 removed outlier: 3.939A pdb=" N ALA h 219 " --> pdb=" O ILE h 216 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG h 220 " --> pdb=" O ASP h 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 216 through 220' Processing helix chain 'h' and resid 236 through 241 Processing helix chain 'h' and resid 242 through 246 removed outlier: 3.902A pdb=" N HIS h 245 " --> pdb=" O ILE h 242 " (cutoff:3.500A) Processing helix chain 'h' and resid 280 through 286 removed outlier: 4.059A pdb=" N GLU h 283 " --> pdb=" O VAL h 280 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU h 284 " --> pdb=" O LEU h 281 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU h 285 " --> pdb=" O ILE h 282 " (cutoff:3.500A) Processing helix chain 'h' and resid 303 through 318 removed outlier: 3.835A pdb=" N HIS h 309 " --> pdb=" O MET h 305 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA h 312 " --> pdb=" O HIS h 308 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA h 318 " --> pdb=" O LEU h 314 " (cutoff:3.500A) Processing helix chain 'h' and resid 352 through 361 removed outlier: 3.621A pdb=" N GLU h 361 " --> pdb=" O VAL h 357 " (cutoff:3.500A) Processing helix chain 'h' and resid 376 through 383 Processing helix chain 'h' and resid 397 through 406 removed outlier: 3.955A pdb=" N TYR h 405 " --> pdb=" O PHE h 401 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 448 removed outlier: 3.690A pdb=" N LYS h 434 " --> pdb=" O THR h 430 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS h 448 " --> pdb=" O GLU h 444 " (cutoff:3.500A) Processing helix chain 'h' and resid 458 through 473 Processing helix chain 'h' and resid 483 through 492 Processing helix chain 'h' and resid 518 through 525 Processing helix chain 'h' and resid 532 through 552 removed outlier: 3.867A pdb=" N LYS h 536 " --> pdb=" O GLU h 532 " (cutoff:3.500A) Processing helix chain 'h' and resid 564 through 573 removed outlier: 3.880A pdb=" N ASP h 568 " --> pdb=" O SER h 564 " (cutoff:3.500A) Processing helix chain 'h' and resid 574 through 575 No H-bonds generated for 'chain 'h' and resid 574 through 575' Processing helix chain 'h' and resid 576 through 579 removed outlier: 3.769A pdb=" N GLY h 579 " --> pdb=" O GLY h 576 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 576 through 579' Processing helix chain 'h' and resid 592 through 596 Processing helix chain 'h' and resid 600 through 607 Processing helix chain 'h' and resid 621 through 669 removed outlier: 3.821A pdb=" N LEU h 645 " --> pdb=" O ILE h 641 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL h 669 " --> pdb=" O GLU h 665 " (cutoff:3.500A) Processing helix chain 'h' and resid 671 through 690 removed outlier: 4.139A pdb=" N THR h 675 " --> pdb=" O ASP h 671 " (cutoff:3.500A) Processing helix chain 'h' and resid 702 through 715 removed outlier: 3.815A pdb=" N ASP h 715 " --> pdb=" O LYS h 711 " (cutoff:3.500A) Processing helix chain 'h' and resid 719 through 727 removed outlier: 4.282A pdb=" N GLU h 727 " --> pdb=" O TRP h 723 " (cutoff:3.500A) Processing helix chain 'h' and resid 734 through 755 Processing helix chain 'h' and resid 755 through 788 Processing helix chain 'h' and resid 802 through 828 Processing helix chain 'k' and resid 53 through 67 Processing helix chain 'k' and resid 71 through 76 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.578A pdb=" N ILE C 91 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.548A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS C 183 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE C 267 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 15 removed outlier: 5.630A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.500A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.910A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.151A pdb=" N LEU E 147 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR E 189 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE E 149 " --> pdb=" O THR E 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.527A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=AB5, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AB6, first strand: chain 'G' and resid 94 through 99 Processing sheet with id=AB7, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB8, first strand: chain 'H' and resid 78 through 82 removed outlier: 6.779A pdb=" N VAL H 78 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL H 147 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE H 80 " --> pdb=" O VAL H 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 50 through 53 removed outlier: 3.776A pdb=" N ALA I 110 " --> pdb=" O VAL I 27 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 9 through 14 Processing sheet with id=AC2, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.140A pdb=" N ILE K 54 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP K 15 " --> pdb=" O GLN K 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 10 removed outlier: 3.946A pdb=" N THR L 6 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 10 " --> pdb=" O ARG L 17 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG L 17 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA L 46 " --> pdb=" O ARG L 17 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL L 19 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS L 44 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N CYS L 21 " --> pdb=" O THR L 42 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR L 42 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS L 59 " --> pdb=" O LEU L 87 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS L 84 " --> pdb=" O MET L 7 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN L 9 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 76 through 79 removed outlier: 3.607A pdb=" N VAL L 76 " --> pdb=" O VAL Q 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA Q 49 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG Q 62 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL Q 47 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ILE Q 64 " --> pdb=" O GLY Q 45 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N GLY Q 45 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR Q 25 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TRP Q 31 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL Q 81 " --> pdb=" O TRP Q 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 74 through 77 Processing sheet with id=AC7, first strand: chain 'M' and resid 89 through 90 removed outlier: 6.074A pdb=" N VAL M 122 " --> pdb=" O GLU M 143 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.554A pdb=" N LEU N 33 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU N 104 " --> pdb=" O PHE N 31 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE N 31 " --> pdb=" O GLU N 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 39 through 42 removed outlier: 5.779A pdb=" N VAL N 89 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU N 75 " --> pdb=" O VAL N 89 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR N 91 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 33 through 37 removed outlier: 4.437A pdb=" N MET O 110 " --> pdb=" O CYS O 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 47 through 52 removed outlier: 3.691A pdb=" N VAL P 49 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 10 through 15 removed outlier: 6.841A pdb=" N TYR S 2 " --> pdb=" O ILE S 41 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE S 41 " --> pdb=" O TYR S 2 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL S 4 " --> pdb=" O LEU S 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 19 through 23 removed outlier: 6.501A pdb=" N TRP S 92 " --> pdb=" O ARG S 68 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG S 68 " --> pdb=" O TRP S 92 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR S 94 " --> pdb=" O HIS S 66 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS S 66 " --> pdb=" O THR S 94 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL S 96 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL S 64 " --> pdb=" O VAL S 96 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE S 98 " --> pdb=" O GLU S 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU S 62 " --> pdb=" O ILE S 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 72 through 78 removed outlier: 4.081A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 3 through 10 removed outlier: 5.779A pdb=" N SER T 101 " --> pdb=" O HIS T 9 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER T 108 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL T 71 " --> pdb=" O SER T 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 82 through 87 Processing sheet with id=AD8, first strand: chain 'U' and resid 11 through 14 removed outlier: 4.252A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP U 80 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL U 62 " --> pdb=" O TRP U 80 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS U 82 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR U 60 " --> pdb=" O LYS U 82 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR U 84 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL U 58 " --> pdb=" O TYR U 84 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR U 86 " --> pdb=" O GLU U 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 67 through 70 Processing sheet with id=AE1, first strand: chain 'V' and resid 65 through 66 removed outlier: 6.874A pdb=" N LYS V 33 " --> pdb=" O VAL V 28 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL V 28 " --> pdb=" O LYS V 33 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE V 35 " --> pdb=" O LYS V 26 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU V 10 " --> pdb=" O PHE V 73 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE V 72 " --> pdb=" O ASP V 81 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS V 79 " --> pdb=" O ASN V 74 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 41 through 46 Processing sheet with id=AE3, first strand: chain 'V' and resid 83 through 87 Processing sheet with id=AE4, first strand: chain 'W' and resid 3 through 8 removed outlier: 7.904A pdb=" N ASN W 5 " --> pdb=" O ASP W 43 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP W 43 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN W 87 " --> pdb=" O LYS W 25 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE W 89 " --> pdb=" O PRO W 27 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP W 76 " --> pdb=" O ASP W 90 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL W 92 " --> pdb=" O ALA W 74 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ALA W 74 " --> pdb=" O VAL W 92 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE W 4 " --> pdb=" O VAL W 64 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 22 through 23 removed outlier: 7.001A pdb=" N LEU X 59 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 30 through 31 removed outlier: 3.521A pdb=" N GLY X 65 " --> pdb=" O VAL X 31 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 13 through 18 Processing sheet with id=AE8, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id=AE9, first strand: chain 'a' and resid 35 through 39 Processing sheet with id=AF1, first strand: chain 'b' and resid 28 through 30 Processing sheet with id=AF2, first strand: chain 'b' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'c' and resid 20 through 25 Processing sheet with id=AF4, first strand: chain 'e' and resid 14 through 16 Processing sheet with id=AF5, first strand: chain 'f' and resid 2 through 4 removed outlier: 5.801A pdb=" N LYS f 2 " --> pdb=" O ARG f 36 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 154 through 156 removed outlier: 6.959A pdb=" N GLY h 155 " --> pdb=" O TYR h 176 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N THR h 178 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY h 177 " --> pdb=" O VAL h 128 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA h 206 " --> pdb=" O ALA h 388 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N MET h 390 " --> pdb=" O ALA h 206 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS h 98 " --> pdb=" O GLY h 389 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N THR h 391 " --> pdb=" O CYS h 98 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA h 100 " --> pdb=" O THR h 391 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL h 410 " --> pdb=" O ILE h 99 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU h 101 " --> pdb=" O VAL h 410 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 326 through 329 Processing sheet with id=AF8, first strand: chain 'h' and resid 419 through 422 removed outlier: 4.186A pdb=" N GLY h 582 " --> pdb=" O ILE h 419 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 419 through 422 removed outlier: 4.186A pdb=" N GLY h 582 " --> pdb=" O ILE h 419 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU h 554 " --> pdb=" O SER h 583 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ARG h 585 " --> pdb=" O LEU h 554 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE h 556 " --> pdb=" O ARG h 585 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR h 587 " --> pdb=" O ILE h 556 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLY h 558 " --> pdb=" O TYR h 587 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER h 589 " --> pdb=" O GLY h 558 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASN h 477 " --> pdb=" O ILE h 502 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR h 504 " --> pdb=" O ASN h 477 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU h 479 " --> pdb=" O THR h 504 " (cutoff:3.500A) 1430 hydrogen bonds defined for protein. 4020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2605 hydrogen bonds 4084 hydrogen bond angles 0 basepair planarities 1032 basepair parallelities 1656 stacking parallelities Total time for adding SS restraints: 160.15 Time building geometry restraints manager: 44.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 13293 1.33 - 1.45: 44997 1.45 - 1.57: 42342 1.57 - 1.70: 6005 1.70 - 1.82: 221 Bond restraints: 106858 Sorted by residual: bond pdb=" C ILE h 243 " pdb=" N PRO h 244 " ideal model delta sigma weight residual 1.334 1.390 -0.057 8.40e-03 1.42e+04 4.58e+01 bond pdb=" N LEU h 730 " pdb=" CA LEU h 730 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.23e-02 6.61e+03 1.44e+01 bond pdb=" N GLU h 732 " pdb=" CA GLU h 732 " ideal model delta sigma weight residual 1.457 1.505 -0.048 1.29e-02 6.01e+03 1.37e+01 bond pdb=" N GLU h 733 " pdb=" CA GLU h 733 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" N HIS h 731 " pdb=" CA HIS h 731 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.23e+01 ... (remaining 106853 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.72: 18707 106.72 - 114.25: 66778 114.25 - 121.79: 48804 121.79 - 129.32: 22681 129.32 - 136.85: 2210 Bond angle restraints: 159180 Sorted by residual: angle pdb=" N LEU h 730 " pdb=" CA LEU h 730 " pdb=" C LEU h 730 " ideal model delta sigma weight residual 111.36 119.85 -8.49 1.09e+00 8.42e-01 6.07e+01 angle pdb=" C GLU h 733 " pdb=" N THR h 734 " pdb=" CA THR h 734 " ideal model delta sigma weight residual 121.54 135.60 -14.06 1.91e+00 2.74e-01 5.42e+01 angle pdb=" C LYS h 800 " pdb=" N GLN h 801 " pdb=" CA GLN h 801 " ideal model delta sigma weight residual 121.54 134.93 -13.39 1.91e+00 2.74e-01 4.91e+01 angle pdb=" N ILE e 32 " pdb=" CA ILE e 32 " pdb=" C ILE e 32 " ideal model delta sigma weight residual 109.34 123.00 -13.66 2.08e+00 2.31e-01 4.31e+01 angle pdb=" C LYS h 288 " pdb=" N GLU h 289 " pdb=" CA GLU h 289 " ideal model delta sigma weight residual 126.86 136.85 -9.99 1.57e+00 4.06e-01 4.05e+01 ... (remaining 159175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 60521 35.89 - 71.79: 6888 71.79 - 107.68: 783 107.68 - 143.58: 8 143.58 - 179.47: 10 Dihedral angle restraints: 68210 sinusoidal: 55726 harmonic: 12484 Sorted by residual: dihedral pdb=" C HIS h 731 " pdb=" N HIS h 731 " pdb=" CA HIS h 731 " pdb=" CB HIS h 731 " ideal model delta harmonic sigma weight residual -122.60 -145.54 22.94 0 2.50e+00 1.60e-01 8.42e+01 dihedral pdb=" CA GLU I 107 " pdb=" C GLU I 107 " pdb=" N VAL I 108 " pdb=" CA VAL I 108 " ideal model delta harmonic sigma weight residual -180.00 -134.27 -45.73 0 5.00e+00 4.00e-02 8.36e+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 42.26 157.74 1 1.50e+01 4.44e-03 8.22e+01 ... (remaining 68207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 20151 0.169 - 0.338: 99 0.338 - 0.507: 1 0.507 - 0.676: 0 0.676 - 0.844: 1 Chirality restraints: 20252 Sorted by residual: chirality pdb=" CA HIS h 731 " pdb=" N HIS h 731 " pdb=" C HIS h 731 " pdb=" CB HIS h 731 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb=" C3' A A 613 " pdb=" C4' A A 613 " pdb=" O3' A A 613 " pdb=" C2' A A 613 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C1' G A2112 " pdb=" O4' G A2112 " pdb=" C2' G A2112 " pdb=" N9 G A2112 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 20249 not shown) Planarity restraints: 9018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 107 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C GLU I 107 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU I 107 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL I 108 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 26 " -0.040 2.00e-02 2.50e+03 1.85e-02 1.02e+01 pdb=" N9 G A 26 " 0.047 2.00e-02 2.50e+03 pdb=" C8 G A 26 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G A 26 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G A 26 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G A 26 " -0.000 2.00e-02 2.50e+03 pdb=" O6 G A 26 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G A 26 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A 26 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G A 26 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 26 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G A 26 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1433 " -0.044 2.00e-02 2.50e+03 1.92e-02 1.01e+01 pdb=" N9 A A1433 " 0.041 2.00e-02 2.50e+03 pdb=" C8 A A1433 " 0.011 2.00e-02 2.50e+03 pdb=" N7 A A1433 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A A1433 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A1433 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A A1433 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A A1433 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A1433 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A1433 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A A1433 " 0.005 2.00e-02 2.50e+03 ... (remaining 9015 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 2483 2.64 - 3.20: 75417 3.20 - 3.77: 200030 3.77 - 4.33: 267550 4.33 - 4.90: 360610 Nonbonded interactions: 906090 Sorted by model distance: nonbonded pdb=" OP2 C A1153 " pdb="MG MG A3038 " model vdw 2.070 2.170 nonbonded pdb=" OP1 C A1774 " pdb="MG MG A3028 " model vdw 2.076 2.170 nonbonded pdb=" OP1 G A1332 " pdb="MG MG A3015 " model vdw 2.078 2.170 nonbonded pdb=" OP2 A A1783 " pdb="MG MG A3023 " model vdw 2.080 2.170 nonbonded pdb=" OP2 A A 943 " pdb="MG MG A3032 " model vdw 2.080 2.170 ... (remaining 906085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.080 Extract box with map and model: 11.140 Check model and map are aligned: 1.070 Set scattering table: 0.700 Process input model: 355.530 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 374.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.005 0.059 106858 Z= 0.312 Angle : 0.783 14.061 159180 Z= 0.403 Chirality : 0.044 0.844 20252 Planarity : 0.006 0.066 9018 Dihedral : 22.592 179.472 60162 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.28 % Favored : 95.44 % Rotamer: Outliers : 0.73 % Allowed : 6.35 % Favored : 92.92 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.10), residues: 4318 helix: -2.44 (0.10), residues: 1395 sheet: -1.20 (0.17), residues: 766 loop : -2.18 (0.11), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP h 349 HIS 0.021 0.001 HIS C 53 PHE 0.025 0.002 PHE h 684 TYR 0.025 0.002 TYR h 405 ARG 0.016 0.001 ARG h 657 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 999 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8048 (mt-10) REVERT: C 161 TYR cc_start: 0.8572 (p90) cc_final: 0.8336 (p90) REVERT: C 177 ARG cc_start: 0.8969 (tpt90) cc_final: 0.8686 (tpt90) REVERT: C 185 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7678 (tm-30) REVERT: C 225 MET cc_start: 0.8525 (mtm) cc_final: 0.8113 (mtp) REVERT: C 270 ARG cc_start: 0.8263 (mmm160) cc_final: 0.8029 (ttt90) REVERT: D 14 ILE cc_start: 0.9217 (mm) cc_final: 0.8980 (mm) REVERT: D 94 GLN cc_start: 0.8660 (tt0) cc_final: 0.8393 (tt0) REVERT: D 161 MET cc_start: 0.8978 (mtt) cc_final: 0.8731 (mtt) REVERT: D 169 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8201 (ttt-90) REVERT: D 174 SER cc_start: 0.9070 (m) cc_final: 0.8632 (t) REVERT: E 57 LYS cc_start: 0.8951 (tptt) cc_final: 0.8729 (tttm) REVERT: E 136 GLN cc_start: 0.7621 (tp40) cc_final: 0.6941 (tp-100) REVERT: E 195 GLN cc_start: 0.8730 (mt0) cc_final: 0.8409 (mt0) REVERT: F 21 ASN cc_start: 0.8040 (t0) cc_final: 0.7831 (t0) REVERT: F 27 GLN cc_start: 0.7397 (mt0) cc_final: 0.7097 (mt0) REVERT: F 100 PHE cc_start: 0.8435 (t80) cc_final: 0.8164 (t80) REVERT: F 127 ASN cc_start: 0.8029 (m-40) cc_final: 0.7823 (m-40) REVERT: F 128 TYR cc_start: 0.7920 (t80) cc_final: 0.7496 (t80) REVERT: G 2 SER cc_start: 0.8313 (t) cc_final: 0.7972 (p) REVERT: G 30 ASN cc_start: 0.7654 (t0) cc_final: 0.7418 (t0) REVERT: G 74 SER cc_start: 0.8748 (m) cc_final: 0.8325 (p) REVERT: G 128 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7669 (tp40) REVERT: G 147 ASP cc_start: 0.8370 (m-30) cc_final: 0.8091 (m-30) REVERT: H 1 MET cc_start: 0.7584 (ttm) cc_final: 0.6460 (ttt) REVERT: H 22 LYS cc_start: 0.8769 (mmtp) cc_final: 0.8562 (mmtp) REVERT: H 57 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7838 (ttpp) REVERT: H 121 VAL cc_start: 0.6186 (t) cc_final: 0.5953 (p) REVERT: H 129 GLU cc_start: 0.5662 (mm-30) cc_final: 0.5459 (mm-30) REVERT: I 38 MET cc_start: -0.0046 (mmm) cc_final: -0.0317 (ppp) REVERT: I 52 MET cc_start: 0.1075 (tpp) cc_final: 0.0435 (tpp) REVERT: K 74 TYR cc_start: 0.8955 (m-80) cc_final: 0.8601 (m-80) REVERT: K 99 ARG cc_start: 0.8491 (mmm160) cc_final: 0.8241 (mmm-85) REVERT: K 118 MET cc_start: 0.8180 (mtt) cc_final: 0.7567 (mtm) REVERT: L 8 LEU cc_start: 0.9125 (mp) cc_final: 0.8891 (mt) REVERT: L 40 LYS cc_start: 0.8716 (tptt) cc_final: 0.8214 (tptm) REVERT: L 93 GLN cc_start: 0.8856 (mm110) cc_final: 0.8399 (mm-40) REVERT: L 115 ILE cc_start: 0.9258 (mt) cc_final: 0.8944 (mm) REVERT: M 67 THR cc_start: 0.9006 (p) cc_final: 0.8727 (p) REVERT: N 88 ASN cc_start: 0.8586 (m-40) cc_final: 0.8102 (m110) REVERT: O 106 ASP cc_start: 0.8741 (p0) cc_final: 0.8523 (p0) REVERT: O 107 ASN cc_start: 0.8287 (t0) cc_final: 0.7605 (t0) REVERT: P 21 LEU cc_start: 0.8726 (mt) cc_final: 0.8140 (mt) REVERT: Q 7 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8118 (tm-30) REVERT: Q 29 LYS cc_start: 0.8287 (mttt) cc_final: 0.7986 (mmmt) REVERT: Q 68 GLU cc_start: 0.6276 (tp30) cc_final: 0.5171 (tp30) REVERT: Q 82 ASP cc_start: 0.8799 (t70) cc_final: 0.8571 (t0) REVERT: Q 94 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8457 (mmtt) REVERT: Q 98 TYR cc_start: 0.9193 (m-10) cc_final: 0.8829 (m-80) REVERT: Q 106 LYS cc_start: 0.3490 (mttt) cc_final: 0.3066 (mttm) REVERT: R 4 VAL cc_start: 0.9350 (t) cc_final: 0.9094 (p) REVERT: R 32 TYR cc_start: 0.9083 (t80) cc_final: 0.8837 (t80) REVERT: R 91 ASP cc_start: 0.8341 (p0) cc_final: 0.8088 (p0) REVERT: R 110 VAL cc_start: 0.9310 (t) cc_final: 0.8969 (p) REVERT: S 11 GLN cc_start: 0.8870 (mt0) cc_final: 0.8606 (mt0) REVERT: S 26 ASP cc_start: 0.7704 (p0) cc_final: 0.7341 (p0) REVERT: S 73 LYS cc_start: 0.7757 (tttp) cc_final: 0.7536 (mttm) REVERT: S 78 ARG cc_start: 0.8827 (tpp-160) cc_final: 0.8620 (ttm-80) REVERT: T 8 ARG cc_start: 0.8850 (mtp-110) cc_final: 0.8598 (mtp85) REVERT: T 55 ILE cc_start: 0.9501 (mt) cc_final: 0.9288 (mm) REVERT: T 88 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8161 (mtp85) REVERT: U 4 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8072 (tt0) REVERT: U 73 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8236 (ttm110) REVERT: U 86 THR cc_start: 0.9182 (m) cc_final: 0.8515 (p) REVERT: V 6 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7852 (mtm-85) REVERT: V 9 ASP cc_start: 0.8204 (m-30) cc_final: 0.7735 (m-30) REVERT: W 24 ASN cc_start: 0.8572 (t0) cc_final: 0.8309 (t0) REVERT: W 46 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8498 (mtmm) REVERT: W 48 MET cc_start: 0.8736 (tpt) cc_final: 0.8453 (tpp) REVERT: X 78 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8117 (mmtp) REVERT: Y 59 ILE cc_start: 0.9013 (mt) cc_final: 0.8738 (mt) REVERT: Z 34 SER cc_start: 0.8287 (p) cc_final: 0.7521 (m) REVERT: Z 36 GLN cc_start: 0.7048 (tt0) cc_final: 0.6131 (tm-30) REVERT: d 15 SER cc_start: 0.8800 (m) cc_final: 0.8588 (m) REVERT: d 33 ARG cc_start: 0.9037 (mtm-85) cc_final: 0.8716 (ttp-110) REVERT: f 13 ASN cc_start: 0.9068 (m110) cc_final: 0.8753 (m-40) REVERT: f 24 ARG cc_start: 0.7976 (mtt-85) cc_final: 0.7585 (mtt-85) REVERT: h 1 MET cc_start: 0.5531 (mmm) cc_final: 0.2862 (ptp) REVERT: h 31 MET cc_start: 0.1234 (tpt) cc_final: 0.0915 (tpt) REVERT: h 35 MET cc_start: 0.1259 (OUTLIER) cc_final: 0.0454 (mpp) REVERT: h 62 ASN cc_start: 0.7178 (t0) cc_final: 0.6739 (m-40) REVERT: h 81 MET cc_start: -0.1020 (mtm) cc_final: -0.1301 (mtm) REVERT: h 86 VAL cc_start: 0.4743 (p) cc_final: 0.4371 (t) REVERT: h 87 GLN cc_start: 0.0964 (mt0) cc_final: 0.0045 (mp10) REVERT: h 161 MET cc_start: 0.2861 (ttm) cc_final: 0.2656 (mtp) REVERT: h 305 MET cc_start: 0.1955 (pmm) cc_final: 0.1704 (ttm) REVERT: h 381 PHE cc_start: 0.5595 (m-10) cc_final: 0.5338 (m-10) REVERT: h 384 TYR cc_start: 0.3906 (m-80) cc_final: 0.3001 (m-80) REVERT: h 479 LEU cc_start: 0.5193 (mt) cc_final: 0.4649 (mt) REVERT: h 708 GLU cc_start: 0.4559 (tm-30) cc_final: 0.3774 (mm-30) REVERT: h 762 PHE cc_start: 0.1766 (t80) cc_final: 0.1255 (m-10) REVERT: h 782 MET cc_start: 0.3818 (mmm) cc_final: 0.3250 (tmm) REVERT: h 810 MET cc_start: 0.1601 (tpt) cc_final: 0.1359 (ptt) REVERT: k 64 PHE cc_start: 0.7454 (m-10) cc_final: 0.7175 (m-10) outliers start: 26 outliers final: 6 residues processed: 1019 average time/residue: 1.0266 time to fit residues: 1717.4651 Evaluate side-chains 706 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 699 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain h residue 35 MET Chi-restraints excluded: chain h residue 818 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 611 optimal weight: 20.0000 chunk 548 optimal weight: 20.0000 chunk 304 optimal weight: 0.0170 chunk 187 optimal weight: 20.0000 chunk 370 optimal weight: 4.9990 chunk 293 optimal weight: 20.0000 chunk 567 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 345 optimal weight: 10.0000 chunk 422 optimal weight: 2.9990 chunk 657 optimal weight: 5.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 GLN D 136 ASN D 140 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS F 23 ASN F 63 GLN G 38 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN J 12 GLN J 19 ASN J 30 GLN K 128 ASN ** L 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN N 3 GLN O 18 GLN O 62 ASN P 61 GLN Q 52 ASN Q 75 GLN R 81 ASN S 82 HIS U 92 ASN V 40 ASN V 74 ASN Y 6 GLN ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN Z 58 ASN ** h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 354 HIS h 415 ASN h 520 GLN h 533 GLN h 629 ASN h 638 ASN h 662 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 106858 Z= 0.216 Angle : 0.553 11.537 159180 Z= 0.290 Chirality : 0.035 0.253 20252 Planarity : 0.005 0.056 9018 Dihedral : 23.037 179.429 51695 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.33 % Favored : 95.53 % Rotamer: Outliers : 2.71 % Allowed : 12.75 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.78 (0.12), residues: 4318 helix: -0.56 (0.13), residues: 1445 sheet: -1.04 (0.18), residues: 781 loop : -1.63 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP k 74 HIS 0.008 0.001 HIS h 731 PHE 0.024 0.001 PHE h 149 TYR 0.013 0.001 TYR F 8 ARG 0.006 0.000 ARG h 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 745 time to evaluate : 4.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 TYR cc_start: 0.8403 (p90) cc_final: 0.8167 (p90) REVERT: C 175 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7620 (ttm-80) REVERT: C 181 MET cc_start: 0.8387 (mmt) cc_final: 0.8089 (mmp) REVERT: C 270 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7855 (ttt90) REVERT: D 94 GLN cc_start: 0.8864 (tt0) cc_final: 0.8617 (tt0) REVERT: D 161 MET cc_start: 0.8937 (mtt) cc_final: 0.8711 (mtt) REVERT: D 174 SER cc_start: 0.8966 (m) cc_final: 0.8137 (t) REVERT: D 200 ASP cc_start: 0.8119 (m-30) cc_final: 0.7906 (m-30) REVERT: E 88 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7828 (mmt180) REVERT: E 136 GLN cc_start: 0.7531 (tp40) cc_final: 0.7270 (tp-100) REVERT: F 21 ASN cc_start: 0.8060 (t0) cc_final: 0.7730 (t0) REVERT: F 27 GLN cc_start: 0.7803 (mt0) cc_final: 0.7262 (mt0) REVERT: F 38 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7411 (ttp) REVERT: F 81 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7584 (tm-30) REVERT: F 100 PHE cc_start: 0.8432 (t80) cc_final: 0.8209 (t80) REVERT: F 128 TYR cc_start: 0.7880 (t80) cc_final: 0.7613 (t80) REVERT: G 2 SER cc_start: 0.8323 (t) cc_final: 0.8013 (p) REVERT: G 30 ASN cc_start: 0.7733 (t0) cc_final: 0.7526 (t0) REVERT: G 74 SER cc_start: 0.8732 (m) cc_final: 0.8356 (p) REVERT: G 95 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7752 (ttm-80) REVERT: G 147 ASP cc_start: 0.8438 (m-30) cc_final: 0.8173 (m-30) REVERT: H 33 GLN cc_start: 0.8697 (mt0) cc_final: 0.8423 (mt0) REVERT: H 40 THR cc_start: 0.7586 (p) cc_final: 0.7374 (m) REVERT: H 143 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.5810 (mt) REVERT: I 38 MET cc_start: 0.0383 (mmm) cc_final: 0.0165 (ppp) REVERT: J 40 LYS cc_start: 0.4891 (tppt) cc_final: 0.4365 (ttmt) REVERT: K 16 TYR cc_start: 0.9008 (m-80) cc_final: 0.8686 (m-10) REVERT: K 74 TYR cc_start: 0.8976 (m-80) cc_final: 0.8628 (m-80) REVERT: K 118 MET cc_start: 0.8168 (mtt) cc_final: 0.7916 (mtm) REVERT: L 4 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7644 (tt0) REVERT: L 8 LEU cc_start: 0.9138 (mp) cc_final: 0.8851 (mt) REVERT: L 100 PHE cc_start: 0.8084 (m-80) cc_final: 0.7724 (m-80) REVERT: L 114 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8311 (ttmt) REVERT: L 115 ILE cc_start: 0.9351 (mt) cc_final: 0.9148 (mm) REVERT: M 67 THR cc_start: 0.9038 (p) cc_final: 0.8765 (p) REVERT: N 88 ASN cc_start: 0.8531 (m-40) cc_final: 0.8236 (m110) REVERT: P 21 LEU cc_start: 0.8377 (mt) cc_final: 0.8141 (mt) REVERT: P 89 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6853 (t0) REVERT: Q 7 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7908 (tm-30) REVERT: Q 39 ARG cc_start: 0.6063 (ttp-170) cc_final: 0.5045 (ttm-80) REVERT: Q 68 GLU cc_start: 0.6188 (tp30) cc_final: 0.5003 (tp30) REVERT: Q 82 ASP cc_start: 0.8838 (t70) cc_final: 0.8613 (t0) REVERT: Q 98 TYR cc_start: 0.9215 (m-10) cc_final: 0.8874 (m-80) REVERT: Q 106 LYS cc_start: 0.3308 (mttt) cc_final: 0.2992 (mttt) REVERT: R 4 VAL cc_start: 0.9368 (t) cc_final: 0.9143 (p) REVERT: R 95 LEU cc_start: 0.8931 (mt) cc_final: 0.8634 (mt) REVERT: S 16 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7145 (tp30) REVERT: S 26 ASP cc_start: 0.7810 (p0) cc_final: 0.7592 (p0) REVERT: S 73 LYS cc_start: 0.7878 (tttp) cc_final: 0.7607 (mttm) REVERT: S 85 LYS cc_start: 0.9082 (ptmm) cc_final: 0.8755 (ptmm) REVERT: T 1 MET cc_start: 0.7822 (ppp) cc_final: 0.7043 (ppp) REVERT: T 59 GLU cc_start: 0.7795 (tp30) cc_final: 0.7591 (mm-30) REVERT: T 88 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8241 (mtp85) REVERT: U 4 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7876 (tt0) REVERT: U 24 MET cc_start: 0.8564 (tpp) cc_final: 0.7477 (tpt) REVERT: U 73 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8172 (ttm110) REVERT: U 86 THR cc_start: 0.9331 (m) cc_final: 0.8808 (p) REVERT: V 6 ARG cc_start: 0.8265 (mtt180) cc_final: 0.8042 (mtm-85) REVERT: V 9 ASP cc_start: 0.8054 (m-30) cc_final: 0.7645 (m-30) REVERT: W 24 ASN cc_start: 0.8597 (t0) cc_final: 0.8262 (t0) REVERT: W 46 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8587 (mttp) REVERT: W 48 MET cc_start: 0.8744 (tpt) cc_final: 0.8530 (tpp) REVERT: X 56 ASP cc_start: 0.9025 (p0) cc_final: 0.8798 (p0) REVERT: X 78 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8028 (mmtp) REVERT: Y 59 ILE cc_start: 0.8948 (mt) cc_final: 0.8633 (mt) REVERT: Z 2 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8188 (mttm) REVERT: Z 45 GLN cc_start: 0.7879 (mt0) cc_final: 0.7044 (mt0) REVERT: Z 49 ASP cc_start: 0.8320 (m-30) cc_final: 0.7924 (m-30) REVERT: d 15 SER cc_start: 0.8883 (m) cc_final: 0.8513 (m) REVERT: e 55 LEU cc_start: 0.9186 (mt) cc_final: 0.8953 (mt) REVERT: f 13 ASN cc_start: 0.9100 (m110) cc_final: 0.8787 (m-40) REVERT: f 24 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7760 (mtt-85) REVERT: h 1 MET cc_start: 0.5774 (mmm) cc_final: 0.2748 (ptp) REVERT: h 6 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6245 (mm) REVERT: h 62 ASN cc_start: 0.6831 (t0) cc_final: 0.6362 (m-40) REVERT: h 81 MET cc_start: -0.1352 (mtm) cc_final: -0.1610 (mtm) REVERT: h 87 GLN cc_start: 0.1423 (mt0) cc_final: 0.1146 (mt0) REVERT: h 305 MET cc_start: 0.2168 (pmm) cc_final: 0.1962 (ttm) REVERT: h 384 TYR cc_start: 0.3378 (m-80) cc_final: 0.2690 (m-80) REVERT: h 386 LYS cc_start: 0.6387 (mtpt) cc_final: 0.6175 (tttt) REVERT: h 399 PHE cc_start: 0.6847 (t80) cc_final: 0.6569 (t80) REVERT: h 479 LEU cc_start: 0.5543 (mt) cc_final: 0.5055 (mt) REVERT: h 762 PHE cc_start: 0.1938 (t80) cc_final: 0.1522 (m-10) REVERT: h 782 MET cc_start: 0.3402 (mmm) cc_final: 0.2809 (tmm) REVERT: h 800 LYS cc_start: 0.4378 (ttpt) cc_final: 0.3746 (mmtt) outliers start: 96 outliers final: 59 residues processed: 802 average time/residue: 0.9364 time to fit residues: 1272.1028 Evaluate side-chains 733 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 670 time to evaluate : 4.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 66 ASP Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 191 MET Chi-restraints excluded: chain h residue 265 VAL Chi-restraints excluded: chain h residue 272 VAL Chi-restraints excluded: chain h residue 275 THR Chi-restraints excluded: chain h residue 401 PHE Chi-restraints excluded: chain h residue 408 ASP Chi-restraints excluded: chain h residue 415 ASN Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 620 HIS Chi-restraints excluded: chain h residue 624 THR Chi-restraints excluded: chain h residue 659 ILE Chi-restraints excluded: chain h residue 661 SER Chi-restraints excluded: chain h residue 743 SER Chi-restraints excluded: chain h residue 754 VAL Chi-restraints excluded: chain h residue 818 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 365 optimal weight: 0.0000 chunk 204 optimal weight: 10.0000 chunk 547 optimal weight: 7.9990 chunk 447 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 658 optimal weight: 0.9980 chunk 711 optimal weight: 6.9990 chunk 586 optimal weight: 4.9990 chunk 653 optimal weight: 40.0000 chunk 224 optimal weight: 10.0000 chunk 528 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN I 103 ASN K 128 ASN L 93 GLN O 18 GLN Q 41 GLN T 7 HIS V 40 ASN ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN h 29 ASN ** h 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 629 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 106858 Z= 0.197 Angle : 0.522 10.777 159180 Z= 0.275 Chirality : 0.034 0.253 20252 Planarity : 0.004 0.060 9018 Dihedral : 22.961 179.823 51690 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.48 % Rotamer: Outliers : 2.96 % Allowed : 14.78 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 4318 helix: 0.20 (0.14), residues: 1450 sheet: -0.86 (0.18), residues: 771 loop : -1.37 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.008 0.001 HIS h 731 PHE 0.039 0.001 PHE I 76 TYR 0.011 0.001 TYR F 8 ARG 0.008 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 707 time to evaluate : 4.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8274 (mt-10) REVERT: C 132 MET cc_start: 0.8822 (mtm) cc_final: 0.8548 (mtm) REVERT: C 145 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8100 (mt-10) REVERT: C 175 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7652 (ttm-80) REVERT: C 180 GLU cc_start: 0.8378 (tt0) cc_final: 0.8151 (tt0) REVERT: C 181 MET cc_start: 0.8409 (mmt) cc_final: 0.8112 (mmt) REVERT: C 185 GLU cc_start: 0.8058 (tp30) cc_final: 0.7735 (tp30) REVERT: C 270 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7898 (ttt90) REVERT: D 94 GLN cc_start: 0.8904 (tt0) cc_final: 0.8632 (tt0) REVERT: D 161 MET cc_start: 0.8927 (mtt) cc_final: 0.8692 (mtt) REVERT: D 174 SER cc_start: 0.8965 (m) cc_final: 0.8107 (t) REVERT: E 88 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7856 (mmt180) REVERT: E 136 GLN cc_start: 0.7567 (tp40) cc_final: 0.7306 (tp-100) REVERT: F 21 ASN cc_start: 0.8100 (t0) cc_final: 0.7724 (t0) REVERT: F 27 GLN cc_start: 0.8028 (mt0) cc_final: 0.7647 (mt0) REVERT: F 175 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: G 30 ASN cc_start: 0.7706 (t0) cc_final: 0.7481 (t0) REVERT: G 74 SER cc_start: 0.8718 (m) cc_final: 0.8335 (p) REVERT: G 147 ASP cc_start: 0.8355 (m-30) cc_final: 0.8139 (m-30) REVERT: G 155 GLU cc_start: 0.8139 (pp20) cc_final: 0.7827 (pp20) REVERT: H 33 GLN cc_start: 0.8721 (mt0) cc_final: 0.8487 (mt0) REVERT: I 38 MET cc_start: 0.0544 (mmm) cc_final: 0.0271 (ppp) REVERT: J 17 MET cc_start: 0.2859 (mpp) cc_final: 0.2275 (tmm) REVERT: J 51 LYS cc_start: 0.0081 (mmmt) cc_final: -0.0425 (tptt) REVERT: J 125 MET cc_start: 0.0660 (mtt) cc_final: 0.0448 (mmp) REVERT: K 16 TYR cc_start: 0.8960 (m-80) cc_final: 0.8671 (m-10) REVERT: K 74 TYR cc_start: 0.8972 (m-80) cc_final: 0.8578 (m-80) REVERT: K 86 GLN cc_start: 0.8602 (pt0) cc_final: 0.8293 (pt0) REVERT: K 118 MET cc_start: 0.8277 (mtt) cc_final: 0.8022 (mtm) REVERT: L 4 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7621 (tt0) REVERT: L 8 LEU cc_start: 0.9090 (mp) cc_final: 0.8836 (mt) REVERT: L 93 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8404 (mm110) REVERT: L 100 PHE cc_start: 0.8148 (m-80) cc_final: 0.7803 (m-80) REVERT: M 67 THR cc_start: 0.9028 (p) cc_final: 0.8702 (p) REVERT: N 17 ASN cc_start: 0.9133 (t0) cc_final: 0.8806 (t0) REVERT: Q 7 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7945 (tm-30) REVERT: Q 9 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7525 (mt-10) REVERT: Q 68 GLU cc_start: 0.6183 (tp30) cc_final: 0.5006 (tp30) REVERT: Q 82 ASP cc_start: 0.8835 (t70) cc_final: 0.8618 (t0) REVERT: Q 98 TYR cc_start: 0.9211 (m-10) cc_final: 0.8902 (m-80) REVERT: Q 106 LYS cc_start: 0.3259 (mttt) cc_final: 0.2839 (mttt) REVERT: R 4 VAL cc_start: 0.9364 (t) cc_final: 0.9147 (p) REVERT: R 95 LEU cc_start: 0.8909 (mt) cc_final: 0.8657 (mt) REVERT: R 110 VAL cc_start: 0.9355 (t) cc_final: 0.9007 (p) REVERT: S 26 ASP cc_start: 0.7780 (p0) cc_final: 0.7547 (p0) REVERT: S 73 LYS cc_start: 0.7828 (tttp) cc_final: 0.7557 (mttm) REVERT: T 1 MET cc_start: 0.7640 (ppp) cc_final: 0.6818 (ppp) REVERT: T 88 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8208 (mtp85) REVERT: U 24 MET cc_start: 0.8614 (tpp) cc_final: 0.7431 (tpt) REVERT: U 73 ARG cc_start: 0.8336 (ttm110) cc_final: 0.8127 (ttm110) REVERT: U 86 THR cc_start: 0.9310 (m) cc_final: 0.8789 (p) REVERT: V 6 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7979 (mtm-85) REVERT: V 9 ASP cc_start: 0.8112 (m-30) cc_final: 0.7657 (m-30) REVERT: W 24 ASN cc_start: 0.8501 (t0) cc_final: 0.8223 (t0) REVERT: W 48 MET cc_start: 0.8698 (tpt) cc_final: 0.8454 (tpp) REVERT: X 78 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8082 (mmtp) REVERT: Y 59 ILE cc_start: 0.8865 (mt) cc_final: 0.8545 (mt) REVERT: Z 52 ARG cc_start: 0.8489 (mtt90) cc_final: 0.7740 (mtt-85) REVERT: d 15 SER cc_start: 0.8887 (m) cc_final: 0.8475 (m) REVERT: d 33 ARG cc_start: 0.8963 (mtm-85) cc_final: 0.8658 (ttp-110) REVERT: f 13 ASN cc_start: 0.9076 (m110) cc_final: 0.8749 (m110) REVERT: f 24 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7737 (mtt-85) REVERT: h 1 MET cc_start: 0.5824 (mmm) cc_final: 0.2831 (ptp) REVERT: h 6 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6422 (mm) REVERT: h 62 ASN cc_start: 0.6844 (t0) cc_final: 0.6461 (m110) REVERT: h 81 MET cc_start: -0.0410 (mtm) cc_final: -0.0670 (mtm) REVERT: h 161 MET cc_start: 0.2517 (ttm) cc_final: 0.2101 (mtt) REVERT: h 381 PHE cc_start: 0.5154 (m-10) cc_final: 0.4782 (m-10) REVERT: h 384 TYR cc_start: 0.3381 (m-80) cc_final: 0.2749 (m-80) REVERT: h 386 LYS cc_start: 0.6107 (mtpt) cc_final: 0.5891 (tttt) REVERT: h 479 LEU cc_start: 0.5515 (mt) cc_final: 0.5027 (mt) REVERT: h 762 PHE cc_start: 0.2525 (t80) cc_final: 0.2064 (m-10) outliers start: 105 outliers final: 73 residues processed: 768 average time/residue: 0.9326 time to fit residues: 1228.3616 Evaluate side-chains 737 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 662 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 178 THR Chi-restraints excluded: chain h residue 191 MET Chi-restraints excluded: chain h residue 265 VAL Chi-restraints excluded: chain h residue 275 THR Chi-restraints excluded: chain h residue 401 PHE Chi-restraints excluded: chain h residue 408 ASP Chi-restraints excluded: chain h residue 418 MET Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 620 HIS Chi-restraints excluded: chain h residue 651 VAL Chi-restraints excluded: chain h residue 659 ILE Chi-restraints excluded: chain h residue 661 SER Chi-restraints excluded: chain h residue 683 VAL Chi-restraints excluded: chain h residue 727 GLU Chi-restraints excluded: chain h residue 743 SER Chi-restraints excluded: chain h residue 754 VAL Chi-restraints excluded: chain h residue 818 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 650 optimal weight: 3.9990 chunk 495 optimal weight: 8.9990 chunk 341 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 314 optimal weight: 9.9990 chunk 442 optimal weight: 6.9990 chunk 661 optimal weight: 50.0000 chunk 699 optimal weight: 8.9990 chunk 345 optimal weight: 4.9990 chunk 626 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 66 ASN J 19 ASN K 128 ASN L 88 ASN O 18 GLN P 29 HIS Q 41 GLN V 40 ASN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 629 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 106858 Z= 0.260 Angle : 0.552 10.238 159180 Z= 0.289 Chirality : 0.036 0.264 20252 Planarity : 0.004 0.060 9018 Dihedral : 22.917 179.644 51690 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.23 % Rotamer: Outliers : 3.53 % Allowed : 16.22 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4318 helix: 0.51 (0.14), residues: 1444 sheet: -0.64 (0.18), residues: 813 loop : -1.30 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 248 HIS 0.010 0.001 HIS h 731 PHE 0.017 0.002 PHE h 684 TYR 0.012 0.001 TYR F 8 ARG 0.007 0.000 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 682 time to evaluate : 4.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8248 (mt-10) REVERT: C 145 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 175 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7787 (ttm-80) REVERT: C 181 MET cc_start: 0.8359 (mmt) cc_final: 0.8047 (mmt) REVERT: C 185 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: C 251 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8121 (tm-30) REVERT: C 270 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7874 (ttt90) REVERT: D 94 GLN cc_start: 0.8917 (tt0) cc_final: 0.8649 (tt0) REVERT: D 161 MET cc_start: 0.8900 (mtt) cc_final: 0.8618 (mtt) REVERT: D 174 SER cc_start: 0.8802 (m) cc_final: 0.7919 (t) REVERT: E 88 ARG cc_start: 0.8172 (mmt-90) cc_final: 0.7914 (mmt180) REVERT: E 136 GLN cc_start: 0.7544 (tp40) cc_final: 0.7258 (tp-100) REVERT: E 158 PHE cc_start: 0.8550 (t80) cc_final: 0.8254 (t80) REVERT: F 17 MET cc_start: 0.7981 (tpp) cc_final: 0.7542 (tpp) REVERT: F 27 GLN cc_start: 0.8038 (mt0) cc_final: 0.7332 (mp10) REVERT: F 175 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.6441 (m-80) REVERT: G 74 SER cc_start: 0.8733 (m) cc_final: 0.8350 (p) REVERT: G 95 ARG cc_start: 0.7932 (ttm110) cc_final: 0.7648 (ttm110) REVERT: G 147 ASP cc_start: 0.8401 (m-30) cc_final: 0.8154 (m-30) REVERT: G 155 GLU cc_start: 0.8369 (pp20) cc_final: 0.7858 (pp20) REVERT: H 18 GLN cc_start: 0.7817 (tt0) cc_final: 0.7556 (tm-30) REVERT: H 73 ASN cc_start: 0.5972 (m-40) cc_final: 0.5574 (m-40) REVERT: I 38 MET cc_start: 0.0675 (mmm) cc_final: 0.0356 (tmm) REVERT: J 17 MET cc_start: 0.2922 (mpp) cc_final: 0.2162 (tmm) REVERT: J 40 LYS cc_start: 0.5086 (tppt) cc_final: 0.4635 (ttmt) REVERT: K 16 TYR cc_start: 0.8959 (m-80) cc_final: 0.8653 (m-10) REVERT: K 74 TYR cc_start: 0.9000 (m-80) cc_final: 0.8626 (m-80) REVERT: K 86 GLN cc_start: 0.8638 (pt0) cc_final: 0.8319 (pt0) REVERT: K 118 MET cc_start: 0.8337 (mtt) cc_final: 0.8074 (mtm) REVERT: L 8 LEU cc_start: 0.9106 (mp) cc_final: 0.8862 (mt) REVERT: L 93 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8520 (mm-40) REVERT: L 100 PHE cc_start: 0.8178 (m-80) cc_final: 0.7829 (m-80) REVERT: M 51 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7322 (mt-10) REVERT: M 67 THR cc_start: 0.9046 (p) cc_final: 0.8769 (p) REVERT: N 17 ASN cc_start: 0.9172 (t0) cc_final: 0.8826 (t0) REVERT: P 89 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.7020 (t0) REVERT: Q 9 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7588 (mt-10) REVERT: Q 68 GLU cc_start: 0.6236 (tp30) cc_final: 0.5092 (tp30) REVERT: Q 82 ASP cc_start: 0.8834 (t70) cc_final: 0.8597 (t0) REVERT: Q 98 TYR cc_start: 0.9237 (m-10) cc_final: 0.8906 (m-80) REVERT: Q 106 LYS cc_start: 0.3317 (mttt) cc_final: 0.2841 (mttt) REVERT: R 4 VAL cc_start: 0.9359 (t) cc_final: 0.9133 (p) REVERT: R 110 VAL cc_start: 0.9388 (t) cc_final: 0.9090 (p) REVERT: S 26 ASP cc_start: 0.7787 (p0) cc_final: 0.7463 (p0) REVERT: S 46 GLU cc_start: 0.7713 (tt0) cc_final: 0.7496 (tt0) REVERT: S 70 GLU cc_start: 0.8345 (tp30) cc_final: 0.8137 (tp30) REVERT: S 73 LYS cc_start: 0.7822 (tttp) cc_final: 0.7536 (mttm) REVERT: T 1 MET cc_start: 0.7195 (ppp) cc_final: 0.6874 (ppp) REVERT: T 88 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8287 (mtp85) REVERT: U 24 MET cc_start: 0.8675 (tpp) cc_final: 0.7628 (tpt) REVERT: U 42 GLU cc_start: 0.7626 (mp0) cc_final: 0.7172 (mp0) REVERT: U 73 ARG cc_start: 0.8352 (ttm110) cc_final: 0.7891 (tpp80) REVERT: U 86 THR cc_start: 0.9204 (m) cc_final: 0.8806 (p) REVERT: W 24 ASN cc_start: 0.8493 (t0) cc_final: 0.8204 (t0) REVERT: W 48 MET cc_start: 0.8767 (tpt) cc_final: 0.8500 (tpp) REVERT: X 56 ASP cc_start: 0.9039 (p0) cc_final: 0.8820 (p0) REVERT: X 78 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8124 (mmtp) REVERT: Y 59 ILE cc_start: 0.8904 (mt) cc_final: 0.8585 (mt) REVERT: Z 9 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8501 (mtpp) REVERT: d 15 SER cc_start: 0.8855 (m) cc_final: 0.8435 (m) REVERT: d 33 ARG cc_start: 0.8968 (mtm-85) cc_final: 0.8703 (ttp-110) REVERT: f 13 ASN cc_start: 0.9069 (m110) cc_final: 0.8770 (m110) REVERT: f 24 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7634 (mtt180) REVERT: h 1 MET cc_start: 0.5797 (mmm) cc_final: 0.2824 (ptp) REVERT: h 6 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6407 (mm) REVERT: h 62 ASN cc_start: 0.7043 (t0) cc_final: 0.6659 (m-40) REVERT: h 81 MET cc_start: -0.0449 (mtm) cc_final: -0.0731 (mtm) REVERT: h 87 GLN cc_start: 0.1372 (mt0) cc_final: 0.0317 (mp10) REVERT: h 161 MET cc_start: 0.2724 (ttm) cc_final: 0.1804 (tpp) REVERT: h 207 LEU cc_start: -0.0448 (OUTLIER) cc_final: -0.0706 (tt) REVERT: h 386 LYS cc_start: 0.6277 (mtpt) cc_final: 0.6047 (ttpt) REVERT: h 479 LEU cc_start: 0.5679 (mt) cc_final: 0.5125 (mt) REVERT: h 506 MET cc_start: 0.2484 (mtt) cc_final: 0.2088 (mtt) REVERT: h 762 PHE cc_start: 0.3036 (t80) cc_final: 0.2479 (m-10) REVERT: h 782 MET cc_start: 0.5269 (tmm) cc_final: 0.4731 (mmm) outliers start: 125 outliers final: 85 residues processed: 753 average time/residue: 0.9131 time to fit residues: 1189.8313 Evaluate side-chains 741 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 651 time to evaluate : 4.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 178 THR Chi-restraints excluded: chain h residue 191 MET Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 265 VAL Chi-restraints excluded: chain h residue 275 THR Chi-restraints excluded: chain h residue 401 PHE Chi-restraints excluded: chain h residue 408 ASP Chi-restraints excluded: chain h residue 418 MET Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 620 HIS Chi-restraints excluded: chain h residue 624 THR Chi-restraints excluded: chain h residue 651 VAL Chi-restraints excluded: chain h residue 659 ILE Chi-restraints excluded: chain h residue 661 SER Chi-restraints excluded: chain h residue 683 VAL Chi-restraints excluded: chain h residue 727 GLU Chi-restraints excluded: chain h residue 730 LEU Chi-restraints excluded: chain h residue 743 SER Chi-restraints excluded: chain h residue 754 VAL Chi-restraints excluded: chain h residue 818 LEU Chi-restraints excluded: chain h residue 829 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 582 optimal weight: 7.9990 chunk 397 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 521 optimal weight: 8.9990 chunk 288 optimal weight: 20.0000 chunk 597 optimal weight: 7.9990 chunk 483 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 357 optimal weight: 20.0000 chunk 628 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN Q 41 GLN V 40 ASN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 HIS d 29 GLN h 303 ASN ** h 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 629 ASN h 662 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 106858 Z= 0.330 Angle : 0.603 9.635 159180 Z= 0.313 Chirality : 0.038 0.278 20252 Planarity : 0.005 0.093 9018 Dihedral : 22.937 179.961 51690 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.60 % Rotamer: Outliers : 4.01 % Allowed : 17.26 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 4318 helix: 0.51 (0.14), residues: 1446 sheet: -0.63 (0.18), residues: 803 loop : -1.32 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 248 HIS 0.011 0.001 HIS h 731 PHE 0.024 0.002 PHE h 399 TYR 0.013 0.002 TYR N 91 ARG 0.007 0.001 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 670 time to evaluate : 5.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 ARG cc_start: 0.8069 (ttm170) cc_final: 0.7736 (ttm-80) REVERT: C 181 MET cc_start: 0.8414 (mmt) cc_final: 0.8015 (mmt) REVERT: C 225 MET cc_start: 0.8457 (mtm) cc_final: 0.8081 (mtp) REVERT: C 251 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8114 (tm-30) REVERT: C 270 ARG cc_start: 0.8323 (mmm160) cc_final: 0.7904 (ttt90) REVERT: D 94 GLN cc_start: 0.8971 (tt0) cc_final: 0.8682 (tt0) REVERT: D 161 MET cc_start: 0.8895 (mtt) cc_final: 0.8645 (mtt) REVERT: D 174 SER cc_start: 0.8784 (m) cc_final: 0.7883 (t) REVERT: E 88 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7846 (mmt180) REVERT: E 136 GLN cc_start: 0.7507 (tp40) cc_final: 0.7237 (tp-100) REVERT: E 158 PHE cc_start: 0.8634 (t80) cc_final: 0.8357 (t80) REVERT: F 27 GLN cc_start: 0.7990 (mt0) cc_final: 0.7405 (mp10) REVERT: F 175 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: G 74 SER cc_start: 0.8775 (m) cc_final: 0.8368 (p) REVERT: G 95 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7588 (ttm110) REVERT: G 155 GLU cc_start: 0.8420 (pp20) cc_final: 0.8208 (pp20) REVERT: I 38 MET cc_start: 0.0728 (mmm) cc_final: 0.0522 (tmm) REVERT: J 17 MET cc_start: 0.2767 (mpp) cc_final: 0.2279 (tmm) REVERT: J 40 LYS cc_start: 0.4920 (tppt) cc_final: 0.4477 (ttmt) REVERT: J 79 LEU cc_start: 0.0111 (OUTLIER) cc_final: -0.0236 (tp) REVERT: K 16 TYR cc_start: 0.8960 (m-80) cc_final: 0.8621 (m-10) REVERT: K 118 MET cc_start: 0.8338 (mtt) cc_final: 0.8054 (mtm) REVERT: L 8 LEU cc_start: 0.9136 (mp) cc_final: 0.8896 (mt) REVERT: L 93 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8417 (mm-40) REVERT: L 100 PHE cc_start: 0.8222 (m-80) cc_final: 0.7886 (m-80) REVERT: L 106 GLU cc_start: 0.7871 (mp0) cc_final: 0.7472 (mp0) REVERT: N 17 ASN cc_start: 0.9198 (t0) cc_final: 0.8812 (t0) REVERT: P 80 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7147 (mm-30) REVERT: P 89 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6849 (t0) REVERT: Q 7 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7550 (tm-30) REVERT: Q 8 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9228 (mp) REVERT: Q 11 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7445 (mt-10) REVERT: Q 68 GLU cc_start: 0.6160 (tp30) cc_final: 0.4998 (tp30) REVERT: Q 82 ASP cc_start: 0.8837 (t70) cc_final: 0.8592 (t0) REVERT: Q 98 TYR cc_start: 0.9256 (m-10) cc_final: 0.8909 (m-80) REVERT: Q 106 LYS cc_start: 0.3346 (mttt) cc_final: 0.2937 (mttt) REVERT: R 4 VAL cc_start: 0.9362 (t) cc_final: 0.9110 (p) REVERT: S 70 GLU cc_start: 0.8421 (tp30) cc_final: 0.8189 (tp30) REVERT: S 73 LYS cc_start: 0.7716 (tttp) cc_final: 0.7488 (mttm) REVERT: T 88 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8284 (mtp85) REVERT: U 4 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8081 (tm-30) REVERT: U 24 MET cc_start: 0.8724 (tpp) cc_final: 0.7632 (tpt) REVERT: U 42 GLU cc_start: 0.7549 (mp0) cc_final: 0.7153 (mp0) REVERT: U 73 ARG cc_start: 0.8351 (ttm110) cc_final: 0.7949 (tpp80) REVERT: U 86 THR cc_start: 0.9215 (m) cc_final: 0.8695 (p) REVERT: V 60 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: W 20 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8541 (tt) REVERT: W 24 ASN cc_start: 0.8501 (t0) cc_final: 0.8196 (t0) REVERT: W 48 MET cc_start: 0.8782 (tpt) cc_final: 0.8522 (tpp) REVERT: X 56 ASP cc_start: 0.9028 (p0) cc_final: 0.8778 (p0) REVERT: X 78 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8094 (mmtp) REVERT: Y 59 ILE cc_start: 0.8853 (mt) cc_final: 0.8547 (mt) REVERT: Z 45 GLN cc_start: 0.7791 (mt0) cc_final: 0.6963 (mt0) REVERT: Z 49 ASP cc_start: 0.8360 (m-30) cc_final: 0.7918 (m-30) REVERT: d 15 SER cc_start: 0.8850 (m) cc_final: 0.8429 (m) REVERT: d 33 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.8698 (ttp-110) REVERT: f 13 ASN cc_start: 0.9063 (m110) cc_final: 0.8765 (m110) REVERT: h 1 MET cc_start: 0.5738 (mmm) cc_final: 0.2719 (ptp) REVERT: h 62 ASN cc_start: 0.6568 (t0) cc_final: 0.6015 (m-40) REVERT: h 81 MET cc_start: -0.0527 (mtm) cc_final: -0.0862 (mtm) REVERT: h 87 GLN cc_start: 0.1505 (mt0) cc_final: 0.1015 (mt0) REVERT: h 102 MET cc_start: 0.4063 (ptp) cc_final: 0.3463 (ptm) REVERT: h 161 MET cc_start: 0.2919 (ttm) cc_final: 0.1949 (tpp) REVERT: h 207 LEU cc_start: -0.0366 (OUTLIER) cc_final: -0.0810 (tt) REVERT: h 386 LYS cc_start: 0.6097 (mtpt) cc_final: 0.5881 (tttt) REVERT: h 479 LEU cc_start: 0.5921 (mt) cc_final: 0.5327 (mt) REVERT: h 506 MET cc_start: 0.2516 (mtt) cc_final: 0.2235 (mtt) REVERT: h 762 PHE cc_start: 0.3037 (t80) cc_final: 0.2445 (m-10) REVERT: h 782 MET cc_start: 0.4906 (tmm) cc_final: 0.4410 (mmm) outliers start: 142 outliers final: 110 residues processed: 760 average time/residue: 0.9144 time to fit residues: 1201.0015 Evaluate side-chains 761 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 644 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain V residue 60 GLU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 35 GLU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain a residue 41 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 61 GLU Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 178 THR Chi-restraints excluded: chain h residue 191 MET Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 224 ILE Chi-restraints excluded: chain h residue 265 VAL Chi-restraints excluded: chain h residue 275 THR Chi-restraints excluded: chain h residue 408 ASP Chi-restraints excluded: chain h residue 410 VAL Chi-restraints excluded: chain h residue 418 MET Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 620 HIS Chi-restraints excluded: chain h residue 624 THR Chi-restraints excluded: chain h residue 651 VAL Chi-restraints excluded: chain h residue 659 ILE Chi-restraints excluded: chain h residue 661 SER Chi-restraints excluded: chain h residue 683 VAL Chi-restraints excluded: chain h residue 727 GLU Chi-restraints excluded: chain h residue 743 SER Chi-restraints excluded: chain h residue 754 VAL Chi-restraints excluded: chain h residue 818 LEU Chi-restraints excluded: chain h residue 829 VAL Chi-restraints excluded: chain h residue 831 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 235 optimal weight: 10.0000 chunk 630 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 410 optimal weight: 2.9990 chunk 172 optimal weight: 30.0000 chunk 700 optimal weight: 40.0000 chunk 581 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN Q 41 GLN V 40 ASN Z 36 GLN d 29 GLN h 355 GLN ** h 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 629 ASN ** h 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 106858 Z= 0.297 Angle : 0.578 9.957 159180 Z= 0.301 Chirality : 0.037 0.268 20252 Planarity : 0.004 0.061 9018 Dihedral : 22.939 179.996 51689 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 3.92 % Allowed : 18.93 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 4318 helix: 0.64 (0.14), residues: 1445 sheet: -0.54 (0.18), residues: 801 loop : -1.26 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 248 HIS 0.009 0.001 HIS h 731 PHE 0.021 0.002 PHE h 399 TYR 0.015 0.001 TYR N 91 ARG 0.008 0.000 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 652 time to evaluate : 4.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7744 (ttm-80) REVERT: C 181 MET cc_start: 0.8437 (mmt) cc_final: 0.8113 (mmt) REVERT: C 251 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8149 (tm-30) REVERT: C 270 ARG cc_start: 0.8325 (mmm160) cc_final: 0.8078 (ttt90) REVERT: D 94 GLN cc_start: 0.8964 (tt0) cc_final: 0.8653 (tt0) REVERT: D 161 MET cc_start: 0.8895 (mtt) cc_final: 0.8652 (mtt) REVERT: D 174 SER cc_start: 0.8769 (m) cc_final: 0.7863 (t) REVERT: E 136 GLN cc_start: 0.7507 (tp40) cc_final: 0.7254 (tp-100) REVERT: E 158 PHE cc_start: 0.8645 (t80) cc_final: 0.8362 (t80) REVERT: F 27 GLN cc_start: 0.8092 (mt0) cc_final: 0.7532 (mp10) REVERT: F 44 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.5852 (tp) REVERT: F 175 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: G 74 SER cc_start: 0.8784 (m) cc_final: 0.8363 (p) REVERT: G 155 GLU cc_start: 0.8499 (pp20) cc_final: 0.8267 (pp20) REVERT: I 38 MET cc_start: 0.0744 (mmm) cc_final: 0.0532 (tmm) REVERT: J 17 MET cc_start: 0.2351 (mpp) cc_final: 0.1580 (tmm) REVERT: J 40 LYS cc_start: 0.4930 (tppt) cc_final: 0.4512 (ttmt) REVERT: J 79 LEU cc_start: 0.0465 (OUTLIER) cc_final: 0.0110 (tp) REVERT: K 16 TYR cc_start: 0.8922 (m-80) cc_final: 0.8518 (m-10) REVERT: K 91 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7867 (mm-30) REVERT: K 118 MET cc_start: 0.8336 (mtt) cc_final: 0.8057 (mtm) REVERT: L 8 LEU cc_start: 0.9120 (mp) cc_final: 0.8883 (mt) REVERT: L 93 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8390 (mm110) REVERT: L 100 PHE cc_start: 0.8201 (m-80) cc_final: 0.7879 (m-80) REVERT: L 106 GLU cc_start: 0.7874 (mp0) cc_final: 0.7513 (mp0) REVERT: M 78 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7706 (mmm-85) REVERT: N 17 ASN cc_start: 0.9142 (t0) cc_final: 0.8762 (t0) REVERT: N 115 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6832 (tp30) REVERT: P 89 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6896 (t0) REVERT: Q 7 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7629 (tm-30) REVERT: Q 8 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9138 (mp) REVERT: Q 9 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7708 (mt-10) REVERT: Q 11 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7446 (mt-10) REVERT: Q 68 GLU cc_start: 0.6171 (tp30) cc_final: 0.5025 (tp30) REVERT: Q 82 ASP cc_start: 0.8830 (t70) cc_final: 0.8590 (t0) REVERT: Q 98 TYR cc_start: 0.9237 (m-10) cc_final: 0.8896 (m-80) REVERT: Q 106 LYS cc_start: 0.3472 (mttt) cc_final: 0.3257 (mttt) REVERT: R 4 VAL cc_start: 0.9352 (t) cc_final: 0.9099 (p) REVERT: S 73 LYS cc_start: 0.7709 (tttp) cc_final: 0.7480 (mttm) REVERT: T 88 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8292 (mtp85) REVERT: U 4 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8175 (tm-30) REVERT: U 24 MET cc_start: 0.8675 (tpp) cc_final: 0.7584 (tpt) REVERT: U 42 GLU cc_start: 0.7606 (mp0) cc_final: 0.7269 (mp0) REVERT: U 73 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7793 (tpp80) REVERT: U 86 THR cc_start: 0.9241 (m) cc_final: 0.8692 (p) REVERT: V 60 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: W 20 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8603 (tt) REVERT: W 24 ASN cc_start: 0.8501 (t0) cc_final: 0.8198 (t0) REVERT: W 48 MET cc_start: 0.8774 (tpt) cc_final: 0.8512 (tpp) REVERT: W 59 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7445 (mp0) REVERT: W 76 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: X 56 ASP cc_start: 0.9051 (p0) cc_final: 0.8794 (p0) REVERT: X 78 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8092 (mmtp) REVERT: Y 59 ILE cc_start: 0.8827 (mt) cc_final: 0.8502 (mt) REVERT: Z 9 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8355 (mtpp) REVERT: a 37 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: d 15 SER cc_start: 0.8849 (m) cc_final: 0.8428 (m) REVERT: d 33 ARG cc_start: 0.8947 (mtm-85) cc_final: 0.8691 (ttp-110) REVERT: f 13 ASN cc_start: 0.9049 (m110) cc_final: 0.8730 (m110) REVERT: h 1 MET cc_start: 0.5167 (mmm) cc_final: 0.2632 (ptp) REVERT: h 6 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6347 (mm) REVERT: h 62 ASN cc_start: 0.6675 (t0) cc_final: 0.6102 (m-40) REVERT: h 81 MET cc_start: -0.0538 (mtm) cc_final: -0.0886 (mtm) REVERT: h 87 GLN cc_start: 0.1463 (mt0) cc_final: 0.1098 (mt0) REVERT: h 102 MET cc_start: 0.4101 (ptp) cc_final: 0.3536 (ptm) REVERT: h 161 MET cc_start: 0.3045 (ttm) cc_final: 0.2101 (tpp) REVERT: h 207 LEU cc_start: -0.0370 (OUTLIER) cc_final: -0.0818 (tt) REVERT: h 479 LEU cc_start: 0.5912 (mt) cc_final: 0.5293 (mt) REVERT: h 506 MET cc_start: 0.2209 (mtt) cc_final: 0.1964 (mtt) REVERT: h 595 MET cc_start: 0.4106 (tpt) cc_final: 0.3827 (tpt) REVERT: h 762 PHE cc_start: 0.3032 (t80) cc_final: 0.2444 (m-10) outliers start: 139 outliers final: 106 residues processed: 736 average time/residue: 0.9076 time to fit residues: 1154.2195 Evaluate side-chains 759 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 640 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 117 MET Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain V residue 60 GLU Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 76 ASP Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 71 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 18 LEU Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 178 THR Chi-restraints excluded: chain h residue 191 MET Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 224 ILE Chi-restraints excluded: chain h residue 265 VAL Chi-restraints excluded: chain h residue 275 THR Chi-restraints excluded: chain h residue 376 THR Chi-restraints excluded: chain h residue 408 ASP Chi-restraints excluded: chain h residue 410 VAL Chi-restraints excluded: chain h residue 418 MET Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 557 ILE Chi-restraints excluded: chain h residue 620 HIS Chi-restraints excluded: chain h residue 624 THR Chi-restraints excluded: chain h residue 659 ILE Chi-restraints excluded: chain h residue 661 SER Chi-restraints excluded: chain h residue 683 VAL Chi-restraints excluded: chain h residue 727 GLU Chi-restraints excluded: chain h residue 743 SER Chi-restraints excluded: chain h residue 754 VAL Chi-restraints excluded: chain h residue 818 LEU Chi-restraints excluded: chain h residue 829 VAL Chi-restraints excluded: chain h residue 831 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 675 optimal weight: 0.4980 chunk 78 optimal weight: 10.0000 chunk 399 optimal weight: 9.9990 chunk 511 optimal weight: 20.0000 chunk 396 optimal weight: 20.0000 chunk 589 optimal weight: 2.9990 chunk 391 optimal weight: 20.0000 chunk 697 optimal weight: 0.4980 chunk 436 optimal weight: 5.9990 chunk 425 optimal weight: 6.9990 chunk 322 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 ASN O 18 GLN Q 41 GLN V 40 ASN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 570 GLN h 629 ASN ** h 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 106858 Z= 0.152 Angle : 0.529 10.539 159180 Z= 0.279 Chirality : 0.034 0.252 20252 Planarity : 0.004 0.061 9018 Dihedral : 22.993 179.603 51689 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 3.64 % Allowed : 19.46 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4318 helix: 0.77 (0.14), residues: 1450 sheet: -0.49 (0.18), residues: 792 loop : -1.20 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.006 0.001 HIS e 31 PHE 0.031 0.001 PHE H 46 TYR 0.018 0.001 TYR F 8 ARG 0.006 0.000 ARG T 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 673 time to evaluate : 4.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 TYR cc_start: 0.9009 (t80) cc_final: 0.8456 (t80) REVERT: C 175 ARG cc_start: 0.8034 (ttm170) cc_final: 0.7767 (ttm-80) REVERT: C 181 MET cc_start: 0.8367 (mmt) cc_final: 0.8106 (mmt) REVERT: C 185 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: C 251 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8135 (tm-30) REVERT: C 270 ARG cc_start: 0.8330 (mmm160) cc_final: 0.8101 (ttt90) REVERT: D 94 GLN cc_start: 0.8928 (tt0) cc_final: 0.8660 (tt0) REVERT: D 161 MET cc_start: 0.8852 (mtt) cc_final: 0.8602 (mtt) REVERT: D 174 SER cc_start: 0.8743 (m) cc_final: 0.7878 (t) REVERT: E 136 GLN cc_start: 0.7501 (tp40) cc_final: 0.7222 (tp-100) REVERT: E 158 PHE cc_start: 0.8609 (t80) cc_final: 0.8310 (t80) REVERT: F 17 MET cc_start: 0.7758 (tpp) cc_final: 0.7450 (tpp) REVERT: F 27 GLN cc_start: 0.8067 (mt0) cc_final: 0.7523 (mp10) REVERT: F 175 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6570 (m-80) REVERT: G 74 SER cc_start: 0.8740 (m) cc_final: 0.8339 (p) REVERT: G 155 GLU cc_start: 0.8470 (pp20) cc_final: 0.8255 (pp20) REVERT: I 38 MET cc_start: 0.0737 (mmm) cc_final: 0.0533 (tmm) REVERT: J 17 MET cc_start: 0.2682 (mpp) cc_final: 0.1949 (tmm) REVERT: J 79 LEU cc_start: 0.0417 (OUTLIER) cc_final: 0.0073 (tp) REVERT: K 16 TYR cc_start: 0.8889 (m-80) cc_final: 0.8554 (m-10) REVERT: K 86 GLN cc_start: 0.8640 (pt0) cc_final: 0.8312 (pt0) REVERT: K 118 MET cc_start: 0.8319 (mtt) cc_final: 0.8060 (mtm) REVERT: L 8 LEU cc_start: 0.9079 (mp) cc_final: 0.8838 (mt) REVERT: L 93 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8423 (mm110) REVERT: L 100 PHE cc_start: 0.8144 (m-80) cc_final: 0.7851 (m-80) REVERT: L 106 GLU cc_start: 0.7857 (mp0) cc_final: 0.7413 (mp0) REVERT: M 78 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7697 (mmm-85) REVERT: N 17 ASN cc_start: 0.9097 (t0) cc_final: 0.8784 (t0) REVERT: P 84 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: P 85 LYS cc_start: 0.8252 (mtmt) cc_final: 0.8046 (ptmt) REVERT: P 89 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6898 (t0) REVERT: Q 7 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7628 (tm-30) REVERT: Q 8 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9130 (mp) REVERT: Q 9 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7621 (mt-10) REVERT: Q 11 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7433 (mt-10) REVERT: Q 68 GLU cc_start: 0.6107 (tp30) cc_final: 0.4954 (tp30) REVERT: Q 82 ASP cc_start: 0.8787 (t70) cc_final: 0.8558 (t0) REVERT: Q 98 TYR cc_start: 0.9155 (m-10) cc_final: 0.8817 (m-80) REVERT: Q 106 LYS cc_start: 0.3364 (mttt) cc_final: 0.3060 (mttt) REVERT: Q 111 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7773 (mtpp) REVERT: R 4 VAL cc_start: 0.9340 (t) cc_final: 0.9093 (p) REVERT: R 49 ASP cc_start: 0.7550 (m-30) cc_final: 0.7197 (m-30) REVERT: T 88 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.8200 (mtp85) REVERT: U 4 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8130 (tm-30) REVERT: U 24 MET cc_start: 0.8639 (tpp) cc_final: 0.7488 (tpt) REVERT: U 42 GLU cc_start: 0.7659 (mp0) cc_final: 0.7294 (mp0) REVERT: U 73 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7996 (tpp80) REVERT: U 86 THR cc_start: 0.9233 (m) cc_final: 0.8674 (p) REVERT: V 60 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: V 88 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6593 (mm-30) REVERT: W 20 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8605 (tt) REVERT: W 24 ASN cc_start: 0.8466 (t0) cc_final: 0.8191 (t0) REVERT: W 48 MET cc_start: 0.8685 (tpt) cc_final: 0.8482 (tpp) REVERT: X 56 ASP cc_start: 0.9070 (p0) cc_final: 0.8854 (p0) REVERT: X 78 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8172 (mmtp) REVERT: Y 59 ILE cc_start: 0.8831 (mt) cc_final: 0.8510 (mt) REVERT: Z 9 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8481 (mtpp) REVERT: Z 52 ARG cc_start: 0.8450 (mtt90) cc_final: 0.7709 (mtt-85) REVERT: a 37 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: d 15 SER cc_start: 0.8854 (m) cc_final: 0.8426 (m) REVERT: e 33 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7397 (pt) REVERT: f 13 ASN cc_start: 0.9041 (m110) cc_final: 0.8732 (m110) REVERT: h 62 ASN cc_start: 0.6913 (t0) cc_final: 0.6324 (m-40) REVERT: h 81 MET cc_start: -0.0548 (mtm) cc_final: -0.0895 (mtm) REVERT: h 87 GLN cc_start: 0.1515 (mt0) cc_final: 0.0987 (mt0) REVERT: h 102 MET cc_start: 0.3828 (ptp) cc_final: 0.3097 (ptm) REVERT: h 161 MET cc_start: 0.2938 (ttm) cc_final: 0.2055 (tpp) REVERT: h 207 LEU cc_start: -0.0405 (OUTLIER) cc_final: -0.0847 (tt) REVERT: h 479 LEU cc_start: 0.5893 (mt) cc_final: 0.5184 (mt) REVERT: h 506 MET cc_start: 0.2527 (mtt) cc_final: 0.2271 (mtt) REVERT: h 595 MET cc_start: 0.4121 (tpt) cc_final: 0.3811 (tpt) REVERT: h 762 PHE cc_start: 0.3125 (t80) cc_final: 0.2520 (m-10) outliers start: 129 outliers final: 95 residues processed: 753 average time/residue: 0.9141 time to fit residues: 1188.9136 Evaluate side-chains 761 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 654 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 27 VAL Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 60 GLU Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 18 LEU Chi-restraints excluded: chain h residue 178 THR Chi-restraints excluded: chain h residue 179 ASN Chi-restraints excluded: chain h residue 191 MET Chi-restraints excluded: chain h residue 207 LEU Chi-restraints excluded: chain h residue 224 ILE Chi-restraints excluded: chain h residue 265 VAL Chi-restraints excluded: chain h residue 275 THR Chi-restraints excluded: chain h residue 393 THR Chi-restraints excluded: chain h residue 401 PHE Chi-restraints excluded: chain h residue 408 ASP Chi-restraints excluded: chain h residue 410 VAL Chi-restraints excluded: chain h residue 418 MET Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 570 GLN Chi-restraints excluded: chain h residue 620 HIS Chi-restraints excluded: chain h residue 624 THR Chi-restraints excluded: chain h residue 651 VAL Chi-restraints excluded: chain h residue 659 ILE Chi-restraints excluded: chain h residue 683 VAL Chi-restraints excluded: chain h residue 727 GLU Chi-restraints excluded: chain h residue 743 SER Chi-restraints excluded: chain h residue 754 VAL Chi-restraints excluded: chain h residue 818 LEU Chi-restraints excluded: chain h residue 829 VAL Chi-restraints excluded: chain h residue 831 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 431 optimal weight: 6.9990 chunk 278 optimal weight: 30.0000 chunk 416 optimal weight: 40.0000 chunk 210 optimal weight: 50.0000 chunk 137 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 443 optimal weight: 10.0000 chunk 475 optimal weight: 0.0670 chunk 345 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 548 optimal weight: 30.0000 overall best weight: 7.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN Q 41 GLN S 12 HIS V 40 ASN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 29 GLN ** h 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 629 ASN ** h 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 106858 Z= 0.315 Angle : 0.589 10.781 159180 Z= 0.305 Chirality : 0.038 0.273 20252 Planarity : 0.005 0.061 9018 Dihedral : 22.909 179.639 51689 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 3.67 % Allowed : 19.66 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4318 helix: 0.74 (0.14), residues: 1446 sheet: -0.51 (0.18), residues: 804 loop : -1.21 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.009 0.001 HIS h 731 PHE 0.023 0.002 PHE h 399 TYR 0.014 0.001 TYR N 91 ARG 0.009 0.001 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 647 time to evaluate : 4.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7759 (ttm-80) REVERT: C 181 MET cc_start: 0.8375 (mmt) cc_final: 0.7992 (mmt) REVERT: C 251 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 270 ARG cc_start: 0.8329 (mmm160) cc_final: 0.8072 (ttt90) REVERT: D 94 GLN cc_start: 0.8965 (tt0) cc_final: 0.8605 (tt0) REVERT: D 161 MET cc_start: 0.8889 (mtt) cc_final: 0.8638 (mtt) REVERT: D 174 SER cc_start: 0.8674 (m) cc_final: 0.7766 (t) REVERT: E 136 GLN cc_start: 0.7507 (tp40) cc_final: 0.7246 (tp-100) REVERT: E 158 PHE cc_start: 0.8634 (t80) cc_final: 0.8372 (t80) REVERT: F 27 GLN cc_start: 0.8073 (mt0) cc_final: 0.7546 (mp10) REVERT: F 44 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.5853 (tp) REVERT: F 175 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: G 74 SER cc_start: 0.8783 (m) cc_final: 0.8360 (p) REVERT: G 155 GLU cc_start: 0.8548 (pp20) cc_final: 0.8332 (pp20) REVERT: I 38 MET cc_start: 0.0747 (mmm) cc_final: 0.0537 (tmm) REVERT: J 17 MET cc_start: 0.2374 (mpp) cc_final: 0.1504 (tmm) REVERT: J 40 LYS cc_start: 0.4788 (tppt) cc_final: 0.4384 (ttmt) REVERT: J 79 LEU cc_start: 0.0449 (OUTLIER) cc_final: 0.0076 (tp) REVERT: K 16 TYR cc_start: 0.8936 (m-80) cc_final: 0.8599 (m-10) REVERT: K 86 GLN cc_start: 0.8611 (pt0) cc_final: 0.8222 (pt0) REVERT: K 91 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7748 (mm-30) REVERT: K 118 MET cc_start: 0.8353 (mtt) cc_final: 0.8075 (mtm) REVERT: L 8 LEU cc_start: 0.9117 (mp) cc_final: 0.8881 (mt) REVERT: L 93 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8306 (mm110) REVERT: L 100 PHE cc_start: 0.8158 (m-80) cc_final: 0.7841 (m-80) REVERT: L 106 GLU cc_start: 0.7869 (mp0) cc_final: 0.7459 (mp0) REVERT: M 78 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7726 (mmm-85) REVERT: N 17 ASN cc_start: 0.9138 (t0) cc_final: 0.8747 (t0) REVERT: N 115 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6834 (tp30) REVERT: P 85 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7996 (ptmt) REVERT: Q 7 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7692 (tm-30) REVERT: Q 8 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9170 (mp) REVERT: Q 9 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7575 (mt-10) REVERT: Q 11 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7554 (mt-10) REVERT: Q 68 GLU cc_start: 0.6177 (tp30) cc_final: 0.4995 (tp30) REVERT: Q 82 ASP cc_start: 0.8830 (t70) cc_final: 0.8589 (t0) REVERT: Q 98 TYR cc_start: 0.9237 (m-10) cc_final: 0.8891 (m-80) REVERT: Q 111 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7778 (mtpp) REVERT: R 4 VAL cc_start: 0.9355 (t) cc_final: 0.9111 (p) REVERT: T 88 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8284 (mtp85) REVERT: U 4 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8139 (tm-30) REVERT: U 24 MET cc_start: 0.8687 (tpp) cc_final: 0.7501 (tpt) REVERT: U 42 GLU cc_start: 0.7625 (mp0) cc_final: 0.7216 (mp0) REVERT: U 73 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7772 (tpp80) REVERT: U 86 THR cc_start: 0.9236 (m) cc_final: 0.8679 (p) REVERT: V 60 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: W 20 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8578 (tt) REVERT: W 24 ASN cc_start: 0.8494 (t0) cc_final: 0.8188 (t0) REVERT: W 48 MET cc_start: 0.8771 (tpt) cc_final: 0.8472 (tpp) REVERT: X 56 ASP cc_start: 0.9087 (p0) cc_final: 0.8866 (p0) REVERT: X 78 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8096 (mmtp) REVERT: Y 59 ILE cc_start: 0.8817 (mt) cc_final: 0.8491 (mt) REVERT: a 37 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: d 15 SER cc_start: 0.8851 (m) cc_final: 0.8425 (m) REVERT: e 33 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7424 (pt) REVERT: f 13 ASN cc_start: 0.9054 (m110) cc_final: 0.8755 (m110) REVERT: h 1 MET cc_start: 0.5619 (mmm) cc_final: 0.2760 (ptp) REVERT: h 62 ASN cc_start: 0.6670 (t0) cc_final: 0.6116 (m-40) REVERT: h 81 MET cc_start: -0.0544 (mtm) cc_final: -0.0890 (mtm) REVERT: h 87 GLN cc_start: 0.1580 (mt0) cc_final: 0.1116 (mt0) REVERT: h 102 MET cc_start: 0.4048 (ptp) cc_final: 0.3148 (ptm) REVERT: h 161 MET cc_start: 0.2516 (ttm) cc_final: 0.2264 (tpp) REVERT: h 479 LEU cc_start: 0.5866 (mt) cc_final: 0.5231 (mt) REVERT: h 506 MET cc_start: 0.2297 (mtt) cc_final: 0.2033 (mtt) REVERT: h 595 MET cc_start: 0.3927 (tpt) cc_final: 0.3680 (tpt) REVERT: h 762 PHE cc_start: 0.3122 (t80) cc_final: 0.2521 (m-10) outliers start: 130 outliers final: 104 residues processed: 728 average time/residue: 0.9105 time to fit residues: 1148.0247 Evaluate side-chains 749 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 635 time to evaluate : 4.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 34 THR Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain V residue 60 GLU Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 35 GLU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 60 ASP Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 18 LEU Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 178 THR Chi-restraints excluded: chain h residue 179 ASN Chi-restraints excluded: chain h residue 191 MET Chi-restraints excluded: chain h residue 224 ILE Chi-restraints excluded: chain h residue 265 VAL Chi-restraints excluded: chain h residue 275 THR Chi-restraints excluded: chain h residue 376 THR Chi-restraints excluded: chain h residue 393 THR Chi-restraints excluded: chain h residue 408 ASP Chi-restraints excluded: chain h residue 410 VAL Chi-restraints excluded: chain h residue 418 MET Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 620 HIS Chi-restraints excluded: chain h residue 624 THR Chi-restraints excluded: chain h residue 651 VAL Chi-restraints excluded: chain h residue 659 ILE Chi-restraints excluded: chain h residue 683 VAL Chi-restraints excluded: chain h residue 727 GLU Chi-restraints excluded: chain h residue 743 SER Chi-restraints excluded: chain h residue 754 VAL Chi-restraints excluded: chain h residue 818 LEU Chi-restraints excluded: chain h residue 829 VAL Chi-restraints excluded: chain h residue 831 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 634 optimal weight: 1.9990 chunk 668 optimal weight: 50.0000 chunk 609 optimal weight: 6.9990 chunk 650 optimal weight: 7.9990 chunk 391 optimal weight: 30.0000 chunk 283 optimal weight: 10.0000 chunk 510 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 587 optimal weight: 3.9990 chunk 615 optimal weight: 6.9990 chunk 648 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN Q 41 GLN V 40 ASN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 29 GLN h 303 ASN ** h 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 629 ASN ** h 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 106858 Z= 0.220 Angle : 0.556 11.032 159180 Z= 0.291 Chirality : 0.035 0.261 20252 Planarity : 0.004 0.061 9018 Dihedral : 22.948 179.869 51689 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 3.75 % Allowed : 19.94 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4318 helix: 0.74 (0.14), residues: 1452 sheet: -0.53 (0.18), residues: 814 loop : -1.20 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 248 HIS 0.007 0.001 HIS Z 41 PHE 0.026 0.002 PHE h 399 TYR 0.018 0.001 TYR F 8 ARG 0.007 0.000 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 647 time to evaluate : 4.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 TYR cc_start: 0.9036 (t80) cc_final: 0.8470 (t80) REVERT: C 175 ARG cc_start: 0.8067 (ttm170) cc_final: 0.7747 (ttm-80) REVERT: C 181 MET cc_start: 0.8408 (mmt) cc_final: 0.8081 (mmt) REVERT: C 185 GLU cc_start: 0.8084 (tp30) cc_final: 0.7755 (tp30) REVERT: C 251 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8125 (tm-30) REVERT: C 270 ARG cc_start: 0.8342 (mmm160) cc_final: 0.8086 (ttt90) REVERT: D 94 GLN cc_start: 0.8974 (tt0) cc_final: 0.8631 (tt0) REVERT: D 161 MET cc_start: 0.8888 (mtt) cc_final: 0.8641 (mtt) REVERT: D 174 SER cc_start: 0.8668 (m) cc_final: 0.7763 (t) REVERT: E 136 GLN cc_start: 0.7487 (tp40) cc_final: 0.7227 (tp-100) REVERT: E 158 PHE cc_start: 0.8615 (t80) cc_final: 0.8350 (t80) REVERT: F 17 MET cc_start: 0.7726 (tpp) cc_final: 0.7308 (tpp) REVERT: F 27 GLN cc_start: 0.8063 (mt0) cc_final: 0.7533 (mp10) REVERT: F 44 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.5836 (tp) REVERT: F 175 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: G 74 SER cc_start: 0.8764 (m) cc_final: 0.8348 (p) REVERT: G 155 GLU cc_start: 0.8498 (pp20) cc_final: 0.8272 (pp20) REVERT: J 17 MET cc_start: 0.2362 (mpp) cc_final: 0.1422 (tmm) REVERT: J 40 LYS cc_start: 0.4788 (tppt) cc_final: 0.4384 (ttmt) REVERT: J 79 LEU cc_start: 0.0446 (OUTLIER) cc_final: 0.0075 (tp) REVERT: K 16 TYR cc_start: 0.8918 (m-80) cc_final: 0.8583 (m-10) REVERT: K 86 GLN cc_start: 0.8614 (pt0) cc_final: 0.8272 (pt0) REVERT: K 118 MET cc_start: 0.8343 (mtt) cc_final: 0.8068 (mtm) REVERT: L 8 LEU cc_start: 0.9099 (mp) cc_final: 0.8861 (mt) REVERT: L 93 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8333 (mm110) REVERT: L 100 PHE cc_start: 0.8169 (m-80) cc_final: 0.7870 (m-80) REVERT: L 106 GLU cc_start: 0.7862 (mp0) cc_final: 0.7454 (mp0) REVERT: M 78 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7662 (mmm-85) REVERT: N 17 ASN cc_start: 0.9107 (t0) cc_final: 0.8723 (t0) REVERT: N 115 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6918 (tp30) REVERT: P 84 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: P 85 LYS cc_start: 0.8212 (mtmt) cc_final: 0.8000 (ptmt) REVERT: Q 7 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7682 (tm-30) REVERT: Q 8 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9145 (mp) REVERT: Q 9 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7546 (mt-10) REVERT: Q 11 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7552 (mt-10) REVERT: Q 68 GLU cc_start: 0.6183 (tp30) cc_final: 0.5017 (tp30) REVERT: Q 82 ASP cc_start: 0.8814 (t70) cc_final: 0.8578 (t0) REVERT: Q 98 TYR cc_start: 0.9181 (m-10) cc_final: 0.8820 (m-80) REVERT: R 4 VAL cc_start: 0.9347 (t) cc_final: 0.9106 (p) REVERT: R 49 ASP cc_start: 0.7589 (m-30) cc_final: 0.7389 (m-30) REVERT: T 88 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.8257 (mtp85) REVERT: U 4 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8128 (tm-30) REVERT: U 24 MET cc_start: 0.8584 (tpp) cc_final: 0.7488 (tpt) REVERT: U 42 GLU cc_start: 0.7630 (mp0) cc_final: 0.7225 (mp0) REVERT: U 73 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7842 (tpp80) REVERT: U 86 THR cc_start: 0.9234 (m) cc_final: 0.8674 (p) REVERT: V 60 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: W 20 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8597 (tt) REVERT: W 24 ASN cc_start: 0.8480 (t0) cc_final: 0.8178 (t0) REVERT: W 48 MET cc_start: 0.8745 (tpt) cc_final: 0.8541 (tpp) REVERT: X 56 ASP cc_start: 0.9074 (p0) cc_final: 0.8843 (p0) REVERT: X 78 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8129 (mmtp) REVERT: Y 59 ILE cc_start: 0.8835 (mt) cc_final: 0.8516 (mt) REVERT: a 37 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: d 15 SER cc_start: 0.8850 (m) cc_final: 0.8422 (m) REVERT: e 33 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7349 (pt) REVERT: f 13 ASN cc_start: 0.9049 (m110) cc_final: 0.8750 (m110) REVERT: h 1 MET cc_start: 0.5575 (mmm) cc_final: 0.2757 (ptp) REVERT: h 31 MET cc_start: 0.1349 (mmm) cc_final: 0.1059 (tpp) REVERT: h 62 ASN cc_start: 0.6921 (t0) cc_final: 0.6345 (m-40) REVERT: h 81 MET cc_start: -0.0549 (mtm) cc_final: -0.0894 (mtm) REVERT: h 87 GLN cc_start: 0.1632 (mt0) cc_final: 0.1076 (mt0) REVERT: h 102 MET cc_start: 0.4276 (ptp) cc_final: 0.3149 (ptm) REVERT: h 161 MET cc_start: 0.2508 (ttm) cc_final: 0.1493 (mmm) REVERT: h 479 LEU cc_start: 0.5854 (mt) cc_final: 0.5221 (mt) REVERT: h 506 MET cc_start: 0.2505 (mtt) cc_final: 0.2243 (mtt) REVERT: h 595 MET cc_start: 0.3932 (tpt) cc_final: 0.3681 (tpt) REVERT: h 762 PHE cc_start: 0.3129 (t80) cc_final: 0.2524 (m-10) outliers start: 133 outliers final: 110 residues processed: 731 average time/residue: 0.9204 time to fit residues: 1164.4682 Evaluate side-chains 764 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 643 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 135 HIS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 84 GLU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 71 GLU Chi-restraints excluded: chain Q residue 85 SER Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain S residue 45 GLU Chi-restraints excluded: chain S residue 63 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 28 LYS Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 68 ASP Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain V residue 14 LEU Chi-restraints excluded: chain V residue 60 GLU Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 35 GLU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 60 ASP Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 11 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain d residue 9 VAL Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain e residue 54 ASP Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain h residue -1 HIS Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 18 LEU Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 178 THR Chi-restraints excluded: chain h residue 179 ASN Chi-restraints excluded: chain h residue 191 MET Chi-restraints excluded: chain h residue 224 ILE Chi-restraints excluded: chain h residue 265 VAL Chi-restraints excluded: chain h residue 275 THR Chi-restraints excluded: chain h residue 376 THR Chi-restraints excluded: chain h residue 401 PHE Chi-restraints excluded: chain h residue 408 ASP Chi-restraints excluded: chain h residue 410 VAL Chi-restraints excluded: chain h residue 418 MET Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 620 HIS Chi-restraints excluded: chain h residue 624 THR Chi-restraints excluded: chain h residue 651 VAL Chi-restraints excluded: chain h residue 659 ILE Chi-restraints excluded: chain h residue 683 VAL Chi-restraints excluded: chain h residue 727 GLU Chi-restraints excluded: chain h residue 730 LEU Chi-restraints excluded: chain h residue 743 SER Chi-restraints excluded: chain h residue 754 VAL Chi-restraints excluded: chain h residue 818 LEU Chi-restraints excluded: chain h residue 829 VAL Chi-restraints excluded: chain h residue 831 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 427 optimal weight: 9.9990 chunk 687 optimal weight: 40.0000 chunk 419 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 478 optimal weight: 0.0270 chunk 721 optimal weight: 0.7980 chunk 663 optimal weight: 0.9980 chunk 574 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 443 optimal weight: 6.9990 chunk 352 optimal weight: 10.0000 overall best weight: 1.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN H 43 ASN J 19 ASN O 18 GLN Q 41 GLN V 40 ASN b 42 HIS d 29 GLN h 303 ASN ** h 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 629 ASN ** h 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 106858 Z= 0.127 Angle : 0.497 10.174 159180 Z= 0.261 Chirality : 0.032 0.245 20252 Planarity : 0.004 0.060 9018 Dihedral : 22.899 178.360 51689 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 2.40 % Allowed : 21.38 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 4318 helix: 0.97 (0.14), residues: 1457 sheet: -0.36 (0.17), residues: 830 loop : -1.04 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP h 519 HIS 0.005 0.001 HIS e 31 PHE 0.019 0.001 PHE h 399 TYR 0.019 0.001 TYR F 8 ARG 0.009 0.000 ARG F 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8636 Ramachandran restraints generated. 4318 Oldfield, 0 Emsley, 4318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 687 time to evaluate : 5.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7763 (mt-10) REVERT: C 82 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8325 (mt-10) REVERT: C 83 TYR cc_start: 0.9019 (t80) cc_final: 0.8487 (t80) REVERT: C 132 MET cc_start: 0.8790 (mtm) cc_final: 0.8205 (mtm) REVERT: C 145 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7961 (mt-10) REVERT: C 175 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7802 (ttm-80) REVERT: C 181 MET cc_start: 0.8304 (mmt) cc_final: 0.7978 (mmt) REVERT: C 185 GLU cc_start: 0.8065 (tp30) cc_final: 0.7739 (tp30) REVERT: C 270 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7984 (ttt90) REVERT: D 94 GLN cc_start: 0.8952 (tt0) cc_final: 0.8705 (tt0) REVERT: D 174 SER cc_start: 0.8696 (m) cc_final: 0.7799 (t) REVERT: E 136 GLN cc_start: 0.7478 (tp40) cc_final: 0.7201 (tp-100) REVERT: E 158 PHE cc_start: 0.8561 (t80) cc_final: 0.8274 (t80) REVERT: F 17 MET cc_start: 0.7796 (tpp) cc_final: 0.7434 (tpp) REVERT: F 27 GLN cc_start: 0.7856 (mt0) cc_final: 0.7308 (mp10) REVERT: F 175 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6594 (m-80) REVERT: G 74 SER cc_start: 0.8712 (m) cc_final: 0.8303 (p) REVERT: H 47 PHE cc_start: 0.6911 (t80) cc_final: 0.6696 (t80) REVERT: J 17 MET cc_start: 0.3516 (mpp) cc_final: 0.2553 (tmm) REVERT: J 40 LYS cc_start: 0.4935 (tppt) cc_final: 0.4552 (ttmt) REVERT: J 79 LEU cc_start: 0.0403 (OUTLIER) cc_final: 0.0056 (tp) REVERT: K 16 TYR cc_start: 0.8887 (m-80) cc_final: 0.8549 (m-10) REVERT: K 86 GLN cc_start: 0.8645 (pt0) cc_final: 0.8325 (pt0) REVERT: K 118 MET cc_start: 0.8445 (mtt) cc_final: 0.8215 (mtm) REVERT: L 8 LEU cc_start: 0.9017 (mp) cc_final: 0.8773 (mt) REVERT: L 93 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8551 (mm-40) REVERT: L 106 GLU cc_start: 0.7853 (mp0) cc_final: 0.7340 (mp0) REVERT: M 78 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7316 (mmm-85) REVERT: N 17 ASN cc_start: 0.9053 (t0) cc_final: 0.8741 (t0) REVERT: N 22 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7796 (mt0) REVERT: N 70 ASP cc_start: 0.7745 (p0) cc_final: 0.7427 (p0) REVERT: N 106 ASP cc_start: 0.8010 (t70) cc_final: 0.7671 (p0) REVERT: Q 9 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7612 (mt-10) REVERT: Q 68 GLU cc_start: 0.6209 (tp30) cc_final: 0.5046 (tp30) REVERT: Q 82 ASP cc_start: 0.8749 (t70) cc_final: 0.8521 (t0) REVERT: Q 98 TYR cc_start: 0.9092 (m-10) cc_final: 0.8749 (m-80) REVERT: R 49 ASP cc_start: 0.7565 (m-30) cc_final: 0.7351 (m-30) REVERT: T 88 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8141 (mtp85) REVERT: U 4 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8097 (tm-30) REVERT: U 42 GLU cc_start: 0.7639 (mp0) cc_final: 0.7343 (mp0) REVERT: U 73 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7719 (tpp80) REVERT: U 86 THR cc_start: 0.9181 (m) cc_final: 0.8558 (p) REVERT: V 60 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: W 20 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8605 (tt) REVERT: W 48 MET cc_start: 0.8563 (tpt) cc_final: 0.8340 (tpp) REVERT: X 78 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8116 (mmtp) REVERT: Z 45 GLN cc_start: 0.7601 (mt0) cc_final: 0.6611 (mt0) REVERT: Z 49 ASP cc_start: 0.8352 (m-30) cc_final: 0.7853 (m-30) REVERT: a 37 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: a 47 MET cc_start: 0.8682 (mtm) cc_final: 0.8366 (mtm) REVERT: d 15 SER cc_start: 0.8831 (m) cc_final: 0.8377 (m) REVERT: e 32 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.6675 (tp) REVERT: f 13 ASN cc_start: 0.9015 (m110) cc_final: 0.8681 (m110) REVERT: h 1 MET cc_start: 0.4981 (mmm) cc_final: 0.2864 (ptp) REVERT: h 6 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6102 (mm) REVERT: h 62 ASN cc_start: 0.6428 (t0) cc_final: 0.5899 (m-40) REVERT: h 81 MET cc_start: -0.0632 (mtm) cc_final: -0.0973 (mtm) REVERT: h 87 GLN cc_start: 0.1924 (mt0) cc_final: 0.1412 (mt0) REVERT: h 102 MET cc_start: 0.4683 (ptp) cc_final: 0.4168 (ptm) REVERT: h 161 MET cc_start: 0.2219 (ttm) cc_final: 0.1593 (mmm) REVERT: h 479 LEU cc_start: 0.5496 (mt) cc_final: 0.4931 (mt) REVERT: h 506 MET cc_start: 0.2628 (mtt) cc_final: 0.2340 (mtt) REVERT: h 595 MET cc_start: 0.3804 (tpt) cc_final: 0.3518 (tpt) REVERT: h 762 PHE cc_start: 0.3109 (t80) cc_final: 0.2520 (m-10) outliers start: 85 outliers final: 62 residues processed: 743 average time/residue: 0.9267 time to fit residues: 1191.4184 Evaluate side-chains 724 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 654 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 64 ASP Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain S residue 31 GLU Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain U residue 5 GLU Chi-restraints excluded: chain V residue 60 GLU Chi-restraints excluded: chain W residue 20 LEU Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 92 VAL Chi-restraints excluded: chain X residue 64 ASP Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 52 LYS Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain h residue 6 LEU Chi-restraints excluded: chain h residue 153 THR Chi-restraints excluded: chain h residue 191 MET Chi-restraints excluded: chain h residue 265 VAL Chi-restraints excluded: chain h residue 275 THR Chi-restraints excluded: chain h residue 376 THR Chi-restraints excluded: chain h residue 408 ASP Chi-restraints excluded: chain h residue 410 VAL Chi-restraints excluded: chain h residue 418 MET Chi-restraints excluded: chain h residue 459 ILE Chi-restraints excluded: chain h residue 620 HIS Chi-restraints excluded: chain h residue 727 GLU Chi-restraints excluded: chain h residue 730 LEU Chi-restraints excluded: chain h residue 743 SER Chi-restraints excluded: chain h residue 766 VAL Chi-restraints excluded: chain h residue 818 LEU Chi-restraints excluded: chain h residue 829 VAL Chi-restraints excluded: chain h residue 831 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 456 optimal weight: 0.4980 chunk 611 optimal weight: 0.9980 chunk 175 optimal weight: 20.0000 chunk 529 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 575 optimal weight: 0.4980 chunk 240 optimal weight: 10.0000 chunk 590 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 105 optimal weight: 50.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN H 18 GLN O 18 GLN Q 41 GLN V 40 ASN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 29 GLN ** h 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 629 ASN ** h 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.091099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070418 restraints weight = 294377.945| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.35 r_work: 0.3029 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 106858 Z= 0.170 Angle : 0.502 10.305 159180 Z= 0.263 Chirality : 0.032 0.253 20252 Planarity : 0.004 0.060 9018 Dihedral : 22.833 179.263 51689 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 2.40 % Allowed : 21.44 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 4318 helix: 0.97 (0.14), residues: 1465 sheet: -0.33 (0.18), residues: 806 loop : -1.00 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.012 0.001 HIS h 778 PHE 0.021 0.001 PHE h 399 TYR 0.016 0.001 TYR F 8 ARG 0.008 0.000 ARG F 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21235.82 seconds wall clock time: 376 minutes 31.58 seconds (22591.58 seconds total)