Starting phenix.real_space_refine (version: dev) on Sat Dec 17 13:11:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/12_2022/6s0k_10073_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/12_2022/6s0k_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_10073/12_2022/6s0k_10073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/12_2022/6s0k_10073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/12_2022/6s0k_10073_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0k_10073/12_2022/6s0k_10073_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 39.69, per 1000 atoms: 0.40 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: 38.49 Conformation dependent library (CDL) restraints added in 5.3 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: 33.09 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: 164.11 Time building geometry restraints manager: 41.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 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: 55343 35.89 - 71.79: 1895 71.79 - 107.68: 148 107.68 - 143.58: 8 143.58 - 179.47: 10 Dihedral angle restraints: 57404 sinusoidal: 44920 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 57401 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 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. 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 13.900 Check model and map are aligned: 1.080 Convert atoms to be neutral: 0.630 Process input model: 357.130 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 379.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 : 14.550 179.472 49356 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.28 % Favored : 95.44 % Rotamer Outliers : 0.73 % 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 *********************** 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 : 4.485 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 outliers start: 26 outliers final: 6 residues processed: 1019 average time/residue: 1.0157 time to fit residues: 1696.6810 Evaluate side-chains 674 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 668 time to evaluate : 4.446 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6872 time to fit residues: 12.8673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 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: 10.0000 chunk 657 optimal weight: 50.0000 overall best weight: 6.6030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 GLN D 94 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 K 136 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** h 29 ASN ** h 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 520 GLN h 533 GLN h 629 ASN h 638 ASN h 662 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 106858 Z= 0.287 Angle : 0.593 11.660 159180 Z= 0.309 Chirality : 0.037 0.259 20252 Planarity : 0.005 0.058 9018 Dihedral : 13.642 179.665 40878 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.75 % Favored : 95.11 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.11), residues: 4318 helix: -0.69 (0.12), residues: 1429 sheet: -0.99 (0.18), residues: 758 loop : -1.71 (0.12), residues: 2131 *********************** 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 798 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 703 time to evaluate : 4.598 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 outliers start: 95 outliers final: 60 residues processed: 754 average time/residue: 0.9101 time to fit residues: 1166.0519 Evaluate side-chains 704 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 644 time to evaluate : 4.494 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.7280 time to fit residues: 85.9498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 365 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 547 optimal weight: 6.9990 chunk 447 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 658 optimal weight: 7.9990 chunk 711 optimal weight: 7.9990 chunk 586 optimal weight: 5.9990 chunk 653 optimal weight: 30.0000 chunk 224 optimal weight: 10.0000 chunk 528 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** 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 O 18 GLN O 107 ASN P 29 HIS P 61 GLN Q 10 GLN Q 41 GLN S 12 HIS V 40 ASN ** Y 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 303 ASN ** h 415 ASN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 106858 Z= 0.292 Angle : 0.584 11.980 159180 Z= 0.305 Chirality : 0.037 0.266 20252 Planarity : 0.005 0.058 9018 Dihedral : 13.665 179.894 40878 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.89 % Favored : 95.00 % Rotamer Outliers : 2.26 % 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: -1.25 (0.12), residues: 4318 helix: 0.10 (0.13), residues: 1436 sheet: -0.84 (0.18), residues: 775 loop : -1.45 (0.13), residues: 2107 *********************** 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 755 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 675 time to evaluate : 4.624 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 outliers start: 80 outliers final: 33 residues processed: 725 average time/residue: 0.9087 time to fit residues: 1133.8071 Evaluate side-chains 660 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 627 time to evaluate : 4.551 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.7065 time to fit residues: 49.1647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 650 optimal weight: 30.0000 chunk 495 optimal weight: 9.9990 chunk 341 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 314 optimal weight: 9.9990 chunk 442 optimal weight: 9.9990 chunk 661 optimal weight: 50.0000 chunk 699 optimal weight: 10.0000 chunk 345 optimal weight: 4.9990 chunk 626 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 130 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 66 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN O 18 GLN Q 41 GLN V 40 ASN Y 34 HIS d 29 GLN ** 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: 0.8587 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 106858 Z= 0.323 Angle : 0.595 10.873 159180 Z= 0.310 Chirality : 0.038 0.271 20252 Planarity : 0.005 0.058 9018 Dihedral : 13.699 179.792 40878 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.16 % Favored : 94.72 % Rotamer Outliers : 2.40 % 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: -1.09 (0.12), residues: 4318 helix: 0.33 (0.14), residues: 1441 sheet: -0.80 (0.18), residues: 791 loop : -1.42 (0.13), residues: 2086 *********************** 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 729 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 644 time to evaluate : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 58 residues processed: 698 average time/residue: 0.9539 time to fit residues: 1148.7694 Evaluate side-chains 678 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 620 time to evaluate : 4.549 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.7544 time to fit residues: 87.7554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 582 optimal weight: 6.9990 chunk 397 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 521 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 483 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 357 optimal weight: 8.9990 chunk 628 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN Q 41 GLN V 40 ASN 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 106858 Z= 0.336 Angle : 0.606 10.634 159180 Z= 0.315 Chirality : 0.039 0.274 20252 Planarity : 0.005 0.069 9018 Dihedral : 13.757 179.708 40878 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer Outliers : 1.86 % 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: -0.99 (0.12), residues: 4318 helix: 0.40 (0.14), residues: 1446 sheet: -0.71 (0.18), residues: 793 loop : -1.37 (0.13), residues: 2079 *********************** 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 715 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 649 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 39 residues processed: 690 average time/residue: 0.9048 time to fit residues: 1074.1154 Evaluate side-chains 656 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 617 time to evaluate : 4.488 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.7301 time to fit residues: 58.3878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 138 optimal weight: 10.0000 chunk 410 optimal weight: 40.0000 chunk 172 optimal weight: 30.0000 chunk 700 optimal weight: 40.0000 chunk 581 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 367 optimal weight: 6.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- 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 ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN Q 41 GLN V 40 ASN V 54 GLN d 29 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 106858 Z= 0.313 Angle : 0.594 10.256 159180 Z= 0.309 Chirality : 0.038 0.272 20252 Planarity : 0.005 0.090 9018 Dihedral : 13.741 179.654 40878 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer Outliers : 1.81 % 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: -0.91 (0.12), residues: 4318 helix: 0.50 (0.14), residues: 1446 sheet: -0.72 (0.18), residues: 800 loop : -1.31 (0.13), residues: 2072 *********************** 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 704 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 640 time to evaluate : 4.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 32 residues processed: 671 average time/residue: 0.9278 time to fit residues: 1068.8151 Evaluate side-chains 645 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 613 time to evaluate : 4.506 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.7354 time to fit residues: 48.8538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 675 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 399 optimal weight: 10.0000 chunk 511 optimal weight: 0.0470 chunk 396 optimal weight: 20.0000 chunk 589 optimal weight: 0.6980 chunk 391 optimal weight: 30.0000 chunk 697 optimal weight: 9.9990 chunk 436 optimal weight: 0.0020 chunk 425 optimal weight: 20.0000 chunk 322 optimal weight: 0.9980 overall best weight: 2.1488 ------------------------------------------------------------------------------- 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 ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN Q 41 GLN V 40 ASN b 42 HIS d 29 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.066 106858 Z= 0.138 Angle : 0.509 13.992 159180 Z= 0.268 Chirality : 0.032 0.248 20252 Planarity : 0.004 0.073 9018 Dihedral : 13.495 178.741 40878 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer Outliers : 0.87 % 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: -0.56 (0.13), residues: 4318 helix: 0.80 (0.14), residues: 1447 sheet: -0.49 (0.18), residues: 806 loop : -1.14 (0.13), residues: 2065 *********************** 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 706 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 675 time to evaluate : 4.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 688 average time/residue: 0.9042 time to fit residues: 1067.5999 Evaluate side-chains 650 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 634 time to evaluate : 4.567 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.7402 time to fit residues: 27.6609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 431 optimal weight: 7.9990 chunk 278 optimal weight: 30.0000 chunk 416 optimal weight: 30.0000 chunk 210 optimal weight: 50.0000 chunk 137 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 443 optimal weight: 4.9990 chunk 475 optimal weight: 8.9990 chunk 345 optimal weight: 0.0470 chunk 65 optimal weight: 20.0000 chunk 548 optimal weight: 0.0970 overall best weight: 4.4282 ------------------------------------------------------------------------------- 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** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN 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 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 629 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 106858 Z= 0.208 Angle : 0.525 9.683 159180 Z= 0.275 Chirality : 0.034 0.262 20252 Planarity : 0.004 0.072 9018 Dihedral : 13.461 179.928 40878 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer Outliers : 1.04 % 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: -0.51 (0.13), residues: 4318 helix: 0.85 (0.14), residues: 1450 sheet: -0.51 (0.18), residues: 790 loop : -1.10 (0.13), residues: 2078 *********************** 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 671 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 634 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 649 average time/residue: 0.9155 time to fit residues: 1023.0227 Evaluate side-chains 644 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 619 time to evaluate : 4.564 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.7508 time to fit residues: 40.4883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 634 optimal weight: 10.0000 chunk 668 optimal weight: 5.9990 chunk 609 optimal weight: 5.9990 chunk 650 optimal weight: 6.9990 chunk 391 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 chunk 510 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 587 optimal weight: 0.1980 chunk 615 optimal weight: 7.9990 chunk 648 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN V 40 ASN d 29 GLN ** h 415 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 106858 Z= 0.204 Angle : 0.525 9.773 159180 Z= 0.275 Chirality : 0.034 0.262 20252 Planarity : 0.004 0.064 9018 Dihedral : 13.450 179.507 40878 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer Outliers : 0.56 % 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: -0.48 (0.13), residues: 4318 helix: 0.85 (0.14), residues: 1456 sheet: -0.44 (0.18), residues: 797 loop : -1.08 (0.13), residues: 2065 *********************** 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 664 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 644 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 655 average time/residue: 0.9091 time to fit residues: 1021.0918 Evaluate side-chains 635 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 626 time to evaluate : 4.543 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.6950 time to fit residues: 16.8884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 40.0000 chunk 326 optimal weight: 3.9990 chunk 478 optimal weight: 4.9990 chunk 721 optimal weight: 6.9990 chunk 663 optimal weight: 9.9990 chunk 574 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 443 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** H 43 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN V 40 ASN V 54 GLN ** Y 16 ASN ** 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 h 662 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 106858 Z= 0.273 Angle : 0.568 10.622 159180 Z= 0.295 Chirality : 0.036 0.271 20252 Planarity : 0.004 0.066 9018 Dihedral : 13.523 179.842 40878 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer Outliers : 0.54 % 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: -0.54 (0.13), residues: 4318 helix: 0.78 (0.14), residues: 1450 sheet: -0.49 (0.18), residues: 819 loop : -1.09 (0.13), residues: 2049 ********************** 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 640 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 621 time to evaluate : 4.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 629 average time/residue: 0.9706 time to fit residues: 1055.0196 Evaluate side-chains 633 residues out of total 3559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 623 time to evaluate : 4.538 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.7476 time to fit residues: 19.2336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 724 random chunks: chunk 456 optimal weight: 7.9990 chunk 611 optimal weight: 9.9990 chunk 175 optimal weight: 20.0000 chunk 529 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 575 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 590 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 105 optimal weight: 50.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 G 30 ASN H 43 ASN ** J 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN V 40 ASN ** h 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 303 ASN ** h 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 450 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.088212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067631 restraints weight = 295585.988| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.32 r_work: 0.2934 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 106858 Z= 0.343 Angle : 0.619 17.946 159180 Z= 0.320 Chirality : 0.039 0.285 20252 Planarity : 0.005 0.063 9018 Dihedral : 13.676 179.487 40878 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer Outliers : 0.73 % 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: -0.68 (0.13), residues: 4318 helix: 0.61 (0.14), residues: 1462 sheet: -0.55 (0.18), residues: 811 loop : -1.15 (0.13), residues: 2045 =============================================================================== Job complete usr+sys time: 19822.91 seconds wall clock time: 351 minutes 48.46 seconds (21108.46 seconds total)