Starting phenix.real_space_refine (version: dev) on Sat Dec 17 04:43:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2022/6xz7_10655_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2022/6xz7_10655.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2022/6xz7_10655_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2022/6xz7_10655_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2022/6xz7_10655_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2022/6xz7_10655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2022/6xz7_10655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2022/6xz7_10655_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xz7_10655/12_2022/6xz7_10655_updated.pdb" } resolution = 2.1 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= 0.000 sd= 0.037 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 ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E GLU 2": "OE1" <-> "OE2" 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 111": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F ARG 71": "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 115": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 133": "OE1" <-> "OE2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N GLU 49": "OE1" <-> "OE2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N GLU 120": "OE1" <-> "OE2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O GLU 55": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "U GLU 62": "OE1" <-> "OE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W GLU 70": "OE1" <-> "OE2" Residue "W GLU 83": "OE1" <-> "OE2" Residue "W GLU 85": "OE1" <-> "OE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 11": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "b GLU 51": "OE1" <-> "OE2" Residue "c ARG 3": "NH1" <-> "NH2" Residue "c ARG 12": "NH1" <-> "NH2" Residue "c ARG 14": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 41": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 42": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 94915 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 62252 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 277, 'rna2p_pyr': 146, 'rna3p': 17, 'rna3p_pur': 1387, 'rna3p_pyr': 1063} Link IDs: {'rna2p': 429, 'rna3p': 2467} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Conformer: "B" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 277, 'rna2p_pyr': 146, 'rna3p': 17, 'rna3p_pur': 1387, 'rna3p_pyr': 1063} Link IDs: {'rna2p': 429, 'rna3p': 2467} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 bond proxies already assigned to first conformer: 69623 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: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1023 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "I" 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: "J" 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: "K" 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: "L" 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: "M" Number of atoms: 1075 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" 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: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" 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: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" 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: "W" Number of atoms: 580 Number of conformers: 1 Conformer: "A" 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: "X" 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: "Y" 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: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" 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: "b" 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: "c" 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: "d" 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: "e" 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: "f" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "g" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1667 Classifications: {'RNA': 75, 'peptide': 1} Modifications used: {'5*END': 1, 'rna2p': 2, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p': 12, 'rna3p_pur': 30, 'rna3p_pyr': 23} Link IDs: {'rna2p': 10, 'rna3p': 64, None: 1} Not linked: pdbres=" C g 75 " pdbres="31M g 76 " Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 232 Unusual residues: {' MG': 174, 'DI0': 1} Classifications: {'undetermined': 175} Link IDs: {None: 174} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 498 Classifications: {'water': 498} Link IDs: {None: 497} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" P A C A2888 " occ=0.53 ... (38 atoms not shown) pdb=" C6 B C A2888 " occ=0.47 residue: pdb=" N AMEQ D 150 " occ=0.49 ... (8 atoms not shown) pdb=" NE2AMEQ D 150 " occ=0.49 residue: pdb=" N AARG W 41 " occ=0.51 ... (9 atoms not shown) pdb=" NH2AARG W 41 " occ=0.51 residue: pdb=" N AALA Z 2 " occ=0.50 ... (3 atoms not shown) pdb=" CB AALA Z 2 " occ=0.50 residue: pdb=" N ALYS Z 3 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS Z 3 " occ=0.50 Time building chain proxies: 62.85, per 1000 atoms: 0.66 Number of scatterers: 94915 At special positions: 0 Unit cell: (251.12, 227.9, 208.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 3170 15.00 Mg 178 11.99 O 27197 8.00 N 17508 7.00 C 46777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 42.88 Conformation dependent library (CDL) restraints added in 3.3 seconds 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 49 sheets defined 27.7% alpha, 19.8% beta 1041 base pairs and 1710 stacking pairs defined. Time for finding SS restraints: 44.41 Creating SS restraints... Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.920A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.819A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.525A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 39 Processing helix chain 'E' and resid 98 through 114 Processing helix chain 'E' and resid 131 through 140 Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.575A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.550A pdb=" N ASP F 10 " --> pdb=" O ASP F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 19 removed outlier: 3.576A pdb=" N THR F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 42 through 44 No H-bonds generated for 'chain 'F' and resid 42 through 44' Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.874A pdb=" N ASN F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.708A pdb=" N ARG F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 104 " --> pdb=" O PHE F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'G' and resid 59 through 80 removed outlier: 4.573A pdb=" N TRP G 62 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY G 66 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG G 69 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU G 72 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN G 73 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL G 76 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL G 79 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 5 through 21 removed outlier: 3.571A pdb=" N GLY H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 47 Processing helix chain 'H' and resid 57 through 65 removed outlier: 3.744A pdb=" N ALA H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 75 removed outlier: 3.888A pdb=" N ASP H 74 " --> pdb=" O CYS H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 103 removed outlier: 3.665A pdb=" N LYS H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 removed outlier: 3.740A pdb=" N ASP H 124 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA H 127 " --> pdb=" O ASP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'I' and resid 25 through 31 removed outlier: 4.635A pdb=" N GLN I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 48 removed outlier: 5.220A pdb=" N SER I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 83 Processing helix chain 'I' and resid 103 through 116 Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'J' and resid 25 through 37 removed outlier: 4.034A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 97 through 108 removed outlier: 4.234A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.917A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 92 through 97 Processing helix chain 'L' and resid 129 through 138 Processing helix chain 'M' and resid 43 through 56 Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.603A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.270A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 73 through 81 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 122 through 124 No H-bonds generated for 'chain 'N' and resid 122 through 124' Processing helix chain 'O' and resid 3 through 21 removed outlier: 3.537A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 61 removed outlier: 5.846A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 83 Processing helix chain 'O' and resid 102 through 112 Processing helix chain 'P' and resid 3 through 10 Processing helix chain 'P' and resid 54 through 56 No H-bonds generated for 'chain 'P' and resid 54 through 56' Processing helix chain 'P' and resid 98 through 102 Processing helix chain 'P' and resid 105 through 108 Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.568A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 29 Processing helix chain 'Q' and resid 32 through 72 removed outlier: 3.651A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 85 Processing helix chain 'Q' and resid 92 through 101 Processing helix chain 'Q' and resid 103 through 117 Processing helix chain 'S' and resid 14 through 24 removed outlier: 3.762A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 removed outlier: 3.574A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 60 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 4 through 10 removed outlier: 3.980A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 26 Processing helix chain 'T' and resid 40 through 50 Processing helix chain 'U' and resid 51 through 53 No H-bonds generated for 'chain 'U' and resid 51 through 53' Processing helix chain 'U' and resid 67 through 69 No H-bonds generated for 'chain 'U' and resid 67 through 69' Processing helix chain 'V' and resid 14 through 23 Processing helix chain 'V' and resid 44 through 52 removed outlier: 3.533A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 57 Processing helix chain 'X' and resid 53 through 62 Processing helix chain 'X' and resid 64 through 74 Processing helix chain 'Y' and resid 6 through 8 No H-bonds generated for 'chain 'Y' and resid 6 through 8' Processing helix chain 'Y' and resid 11 through 34 Processing helix chain 'Y' and resid 40 through 62 removed outlier: 3.726A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP Y 49 " --> pdb=" O VAL Y 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL Y 50 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS Y 54 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU Y 57 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS Y 60 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA Y 61 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 27 Processing helix chain 'Z' and resid 42 through 50 Processing helix chain 'a' and resid 10 through 19 removed outlier: 4.811A pdb=" N HIS a 19 " --> pdb=" O MET a 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 16 Processing helix chain 'c' and resid 18 through 23 Processing helix chain 'c' and resid 25 through 37 Processing helix chain 'd' and resid 8 through 11 No H-bonds generated for 'chain 'd' and resid 8 through 11' Processing helix chain 'd' and resid 38 through 44 Processing helix chain 'd' and resid 52 through 61 removed outlier: 4.784A pdb=" N GLY d 56 " --> pdb=" O GLY d 53 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE d 59 " --> pdb=" O GLY d 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 33 No H-bonds generated for 'chain 'e' and resid 31 through 33' Processing sheet with id= A, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.641A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'C' and resid 181 through 185 removed outlier: 3.528A pdb=" N ALA C 166 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG C 175 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.772A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 15 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL D 20 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.371A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 115 through 119 removed outlier: 5.725A pdb=" N MET D 165 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE D 118 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY D 163 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= J, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.131A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.590A pdb=" N THR F 155 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR F 35 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS F 87 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU F 66 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 16 through 20 Processing sheet with id= M, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= N, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.544A pdb=" N ARG G 163 " --> pdb=" O GLN G 88 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.615A pdb=" N ARG G 95 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G 113 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.907A pdb=" N SER H 24 " --> pdb=" O VAL H 85 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 111 through 113 Processing sheet with id= R, first strand: chain 'I' and resid 9 through 14 Processing sheet with id= S, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.708A pdb=" N TYR J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL J 18 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= U, first strand: chain 'K' and resid 7 through 9 removed outlier: 6.474A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 74 through 78 removed outlier: 6.636A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE L 77 " --> pdb=" O PHE L 107 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS L 109 " --> pdb=" O ILE L 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.477A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'M' and resid 128 through 132 removed outlier: 3.698A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 39 through 42 removed outlier: 6.945A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP M 92 " --> pdb=" O LYS M 71 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS M 71 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= AA, first strand: chain 'O' and resid 91 through 93 removed outlier: 3.788A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 83 through 88 removed outlier: 6.800A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLU P 44 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE P 64 " --> pdb=" O GLU P 44 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR P 60 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE P 50 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA P 58 " --> pdb=" O ILE P 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 10 through 15 removed outlier: 7.299A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'R' and resid 19 through 23 Processing sheet with id= AE, first strand: chain 'R' and resid 32 through 35 removed outlier: 6.425A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.149A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.808A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'S' and resid 82 through 87 Processing sheet with id= AI, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.615A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'T' and resid 67 through 70 Processing sheet with id= AK, first strand: chain 'U' and resid 22 through 24 removed outlier: 6.076A pdb=" N GLU U 10 " --> pdb=" O PHE U 73 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE U 72 " --> pdb=" O ASP U 81 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'U' and resid 41 through 46 Processing sheet with id= AM, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= AN, first strand: chain 'U' and resid 25 through 28 removed outlier: 6.802A pdb=" N ILE U 35 " --> pdb=" O LYS U 26 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'V' and resid 62 through 65 removed outlier: 7.988A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE V 89 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR V 31 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE V 91 " --> pdb=" O TYR V 31 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'W' and resid 51 through 53 Processing sheet with id= AQ, first strand: chain 'W' and resid 66 through 72 Processing sheet with id= AR, first strand: chain 'X' and resid 13 through 18 Processing sheet with id= AS, first strand: chain 'X' and resid 33 through 40 Processing sheet with id= AT, first strand: chain 'Z' and resid 35 through 39 Processing sheet with id= AU, first strand: chain 'b' and resid 20 through 25 Processing sheet with id= AV, first strand: chain 'e' and resid 2 through 4 Processing sheet with id= AW, first strand: chain 'e' and resid 14 through 19 873 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2614 hydrogen bonds 4046 hydrogen bond angles 0 basepair planarities 1041 basepair parallelities 1712 stacking parallelities Total time for adding SS restraints: 241.89 Time building geometry restraints manager: 46.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 7234 1.27 - 1.40: 32553 1.40 - 1.54: 56259 1.54 - 1.68: 6524 1.68 - 1.82: 153 Bond restraints: 102723 Sorted by residual: bond pdb=" O3' 3TD A1915 " pdb=" P A A1916 " ideal model delta sigma weight residual 1.607 1.315 0.292 1.50e-02 4.44e+03 3.80e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.805 1.422 0.383 2.00e-02 2.50e+03 3.66e+02 bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.805 1.424 0.381 2.00e-02 2.50e+03 3.62e+02 bond pdb=" C4 5MU f 54 " pdb=" C5 5MU f 54 " ideal model delta sigma weight residual 1.805 1.427 0.378 2.00e-02 2.50e+03 3.58e+02 bond pdb=" C4 5MU g 54 " pdb=" C5 5MU g 54 " ideal model delta sigma weight residual 1.805 1.463 0.342 2.00e-02 2.50e+03 2.93e+02 ... (remaining 102718 not shown) Histogram of bond angle deviations from ideal: 86.98 - 97.95: 38 97.95 - 108.92: 40384 108.92 - 119.89: 71889 119.89 - 130.86: 41120 130.86 - 141.83: 1003 Bond angle restraints: 154434 Sorted by residual: angle pdb=" C3' 3TD A1915 " pdb=" O3' 3TD A1915 " pdb=" P A A1916 " ideal model delta sigma weight residual 120.20 89.07 31.13 1.50e+00 4.44e-01 4.31e+02 angle pdb=" O2' C f 51 " pdb=" C2' C f 51 " pdb=" C1' C f 51 " ideal model delta sigma weight residual 108.40 86.98 21.42 1.50e+00 4.44e-01 2.04e+02 angle pdb=" O2' C f 40 " pdb=" C2' C f 40 " pdb=" C1' C f 40 " ideal model delta sigma weight residual 108.40 87.97 20.43 1.50e+00 4.44e-01 1.86e+02 angle pdb=" C4' U g 47 " pdb=" C3' U g 47 " pdb=" O3' U g 47 " ideal model delta sigma weight residual 109.40 129.72 -20.32 1.50e+00 4.44e-01 1.84e+02 angle pdb=" C4' C g 13 " pdb=" C3' C g 13 " pdb=" O3' C g 13 " ideal model delta sigma weight residual 113.00 132.66 -19.66 1.50e+00 4.44e-01 1.72e+02 ... (remaining 154429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 52257 35.85 - 71.71: 1869 71.71 - 107.56: 169 107.56 - 143.41: 17 143.41 - 179.26: 9 Dihedral angle restraints: 54321 sinusoidal: 44820 harmonic: 9501 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 23.09 176.91 1 1.50e+01 4.44e-03 8.53e+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 57.47 142.53 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" O4' U A2321 " pdb=" C1' U A2321 " pdb=" N1 U A2321 " pdb=" C2 U A2321 " ideal model delta sinusoidal sigma weight residual 200.00 60.67 139.33 1 1.50e+01 4.44e-03 7.50e+01 ... (remaining 54318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 19569 0.195 - 0.390: 124 0.390 - 0.585: 23 0.585 - 0.780: 6 0.780 - 0.975: 2 Chirality restraints: 19724 Sorted by residual: chirality pdb=" C3' C g 13 " pdb=" C4' C g 13 " pdb=" O3' C g 13 " pdb=" C2' C g 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.50 -0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" C2' G g 18 " pdb=" C3' G g 18 " pdb=" O2' G g 18 " pdb=" C1' G g 18 " both_signs ideal model delta sigma weight residual False -2.52 -1.72 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C3' U g 47 " pdb=" C4' U g 47 " pdb=" O3' U g 47 " pdb=" C2' U g 47 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.77 2.00e-01 2.50e+01 1.50e+01 ... (remaining 19721 not shown) Planarity restraints: 7764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MA g 58 " 0.876 2.00e-02 2.50e+03 6.96e-01 1.09e+04 pdb=" C4' 1MA g 58 " -0.306 2.00e-02 2.50e+03 pdb=" O4' 1MA g 58 " -0.433 2.00e-02 2.50e+03 pdb=" C3' 1MA g 58 " -0.098 2.00e-02 2.50e+03 pdb=" O3' 1MA g 58 " -1.346 2.00e-02 2.50e+03 pdb=" C2' 1MA g 58 " 0.737 2.00e-02 2.50e+03 pdb=" O2' 1MA g 58 " 0.932 2.00e-02 2.50e+03 pdb=" C1' 1MA g 58 " -0.241 2.00e-02 2.50e+03 pdb=" N9 1MA g 58 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG g 10 " -0.001 2.00e-02 2.50e+03 6.54e-01 9.62e+03 pdb=" C4' 2MG g 10 " 0.476 2.00e-02 2.50e+03 pdb=" O4' 2MG g 10 " 0.766 2.00e-02 2.50e+03 pdb=" C3' 2MG g 10 " -0.561 2.00e-02 2.50e+03 pdb=" O3' 2MG g 10 " -0.686 2.00e-02 2.50e+03 pdb=" C2' 2MG g 10 " -0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG g 10 " 1.063 2.00e-02 2.50e+03 pdb=" C1' 2MG g 10 " 0.160 2.00e-02 2.50e+03 pdb=" N9 2MG g 10 " -1.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' YYG g 37 " 0.072 2.00e-02 2.50e+03 6.35e-01 9.06e+03 pdb=" C4' YYG g 37 " 0.367 2.00e-02 2.50e+03 pdb=" O4' YYG g 37 " 0.596 2.00e-02 2.50e+03 pdb=" C3' YYG g 37 " -0.703 2.00e-02 2.50e+03 pdb=" O3' YYG g 37 " -0.642 2.00e-02 2.50e+03 pdb=" C2' YYG g 37 " -0.116 2.00e-02 2.50e+03 pdb=" O2' YYG g 37 " 1.107 2.00e-02 2.50e+03 pdb=" C1' YYG g 37 " 0.272 2.00e-02 2.50e+03 pdb=" N9 YYG g 37 " -0.954 2.00e-02 2.50e+03 ... (remaining 7761 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 397 2.23 - 2.90: 34443 2.90 - 3.57: 150445 3.57 - 4.23: 315400 4.23 - 4.90: 405152 Nonbonded interactions: 905837 Sorted by model distance: nonbonded pdb=" N2 G A 883 " pdb=" O2 U A 894 " model vdw 1.564 2.496 nonbonded pdb=" OP1 A A2268 " pdb="MG MG A3044 " model vdw 1.586 2.170 nonbonded pdb=" OP1 A A 751 " pdb="MG MG A3012 " model vdw 1.589 2.170 nonbonded pdb=" OP2 A A1189 " pdb="MG MG A3088 " model vdw 1.606 2.170 nonbonded pdb=" OP2 G A1828 " pdb="MG MG A3072 " model vdw 1.620 2.170 ... (remaining 905832 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: 6 Type Number sf(0) Gaussians P 3170 5.49 5 Mg 178 5.21 5 S 85 5.16 5 C 46777 2.51 5 N 17508 2.21 5 O 27197 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=0.47 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: 12.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 31.540 Check model and map are aligned: 1.100 Convert atoms to be neutral: 0.620 Process input model: 450.290 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:9.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 507.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 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 : 0.010 0.383 102723 Z= 0.581 Angle : 0.812 38.533 154434 Z= 0.475 Chirality : 0.049 0.975 19724 Planarity : 0.031 0.696 7764 Dihedral : 14.528 179.265 48203 Min Nonbonded Distance : 1.564 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.83 % Favored : 96.78 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.13), residues: 3287 helix: -2.05 (0.13), residues: 904 sheet: -1.33 (0.18), residues: 695 loop : -1.04 (0.14), residues: 1688 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 642 time to evaluate : 3.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 32 residues processed: 708 average time/residue: 2.0200 time to fit residues: 1875.3029 Evaluate side-chains 577 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 545 time to evaluate : 3.990 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 6 average time/residue: 1.1530 time to fit residues: 14.8156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 537 optimal weight: 2.9990 chunk 482 optimal weight: 0.6980 chunk 267 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 325 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 499 optimal weight: 6.9990 chunk 193 optimal weight: 0.6980 chunk 303 optimal weight: 1.9990 chunk 371 optimal weight: 7.9990 chunk 578 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN D 42 ASN G 104 ASN G 111 HIS N 18 GLN N 23 ASN P 7 GLN P 41 GLN P 75 GLN T 70 HIS U 66 GLN Y 58 ASN Z 49 ASN c 26 ASN d 28 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 102723 Z= 0.174 Angle : 0.718 14.809 154434 Z= 0.400 Chirality : 0.036 0.368 19724 Planarity : 0.008 0.133 7764 Dihedral : 14.184 179.717 41685 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.25 % Favored : 97.63 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3287 helix: -0.21 (0.16), residues: 935 sheet: -0.67 (0.18), residues: 694 loop : -0.48 (0.14), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 552 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 50 residues processed: 614 average time/residue: 1.9150 time to fit residues: 1571.0571 Evaluate side-chains 587 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 537 time to evaluate : 4.243 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 37 residues processed: 14 average time/residue: 0.9143 time to fit residues: 25.7624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 321 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 481 optimal weight: 2.9990 chunk 393 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 579 optimal weight: 1.9990 chunk 626 optimal weight: 50.0000 chunk 516 optimal weight: 5.9990 chunk 574 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 464 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN N 18 GLN N 23 ASN Q 59 GLN U 74 ASN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 102723 Z= 0.269 Angle : 0.766 16.518 154434 Z= 0.420 Chirality : 0.039 0.405 19724 Planarity : 0.009 0.150 7764 Dihedral : 14.032 179.536 41685 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.40 % Favored : 97.47 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3287 helix: 0.33 (0.17), residues: 936 sheet: -0.37 (0.19), residues: 679 loop : -0.32 (0.14), residues: 1672 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 541 time to evaluate : 4.061 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 61 residues processed: 603 average time/residue: 1.9002 time to fit residues: 1532.8054 Evaluate side-chains 590 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 529 time to evaluate : 4.010 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 40 residues processed: 21 average time/residue: 1.0969 time to fit residues: 40.1345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 572 optimal weight: 9.9990 chunk 435 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 389 optimal weight: 6.9990 chunk 581 optimal weight: 4.9990 chunk 615 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 551 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN C 243 HIS F 37 ASN K 29 HIS N 18 GLN N 23 ASN Q 72 ASN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.088 102723 Z= 0.454 Angle : 0.923 20.675 154434 Z= 0.484 Chirality : 0.047 0.389 19724 Planarity : 0.010 0.162 7764 Dihedral : 14.063 178.145 41685 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.28 % Favored : 97.60 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3287 helix: 0.34 (0.17), residues: 927 sheet: -0.35 (0.18), residues: 697 loop : -0.23 (0.15), residues: 1663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 533 time to evaluate : 4.093 Fit side-chains revert: symmetry clash outliers start: 110 outliers final: 68 residues processed: 603 average time/residue: 1.9154 time to fit residues: 1545.3202 Evaluate side-chains 596 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 528 time to evaluate : 4.039 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 45 residues processed: 23 average time/residue: 1.3153 time to fit residues: 48.9021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 512 optimal weight: 7.9990 chunk 349 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 458 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 525 optimal weight: 10.0000 chunk 425 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 552 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN C 142 HIS K 29 HIS N 18 GLN P 75 GLN Q 72 ASN R 86 GLN U 66 GLN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.088 102723 Z= 0.451 Angle : 0.913 19.667 154434 Z= 0.479 Chirality : 0.046 0.385 19724 Planarity : 0.010 0.161 7764 Dihedral : 14.006 178.707 41685 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.44 % Rotamer Outliers : 4.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3287 helix: 0.36 (0.17), residues: 932 sheet: -0.29 (0.18), residues: 697 loop : -0.20 (0.15), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 535 time to evaluate : 4.109 Fit side-chains revert: symmetry clash outliers start: 114 outliers final: 71 residues processed: 611 average time/residue: 1.9458 time to fit residues: 1592.9448 Evaluate side-chains 597 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 526 time to evaluate : 4.050 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 49 residues processed: 23 average time/residue: 1.1486 time to fit residues: 45.7192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 207 optimal weight: 4.9990 chunk 554 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 361 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 616 optimal weight: 0.7980 chunk 511 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 323 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS N 18 GLN P 75 GLN Q 72 ASN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 102723 Z= 0.348 Angle : 0.827 18.937 154434 Z= 0.446 Chirality : 0.042 0.399 19724 Planarity : 0.009 0.155 7764 Dihedral : 13.997 179.439 41685 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.44 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3287 helix: 0.49 (0.17), residues: 932 sheet: -0.26 (0.18), residues: 699 loop : -0.16 (0.15), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 537 time to evaluate : 4.138 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 69 residues processed: 601 average time/residue: 1.9879 time to fit residues: 1589.0156 Evaluate side-chains 602 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 533 time to evaluate : 3.999 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 52 residues processed: 17 average time/residue: 1.1538 time to fit residues: 34.6329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 594 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 351 optimal weight: 3.9990 chunk 450 optimal weight: 0.5980 chunk 348 optimal weight: 2.9990 chunk 518 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 613 optimal weight: 0.6980 chunk 384 optimal weight: 3.9990 chunk 374 optimal weight: 20.0000 chunk 283 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS N 18 GLN P 75 GLN Q 72 ASN U 66 GLN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 102723 Z= 0.192 Angle : 0.700 15.120 154434 Z= 0.394 Chirality : 0.036 0.368 19724 Planarity : 0.008 0.139 7764 Dihedral : 13.875 177.912 41685 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.19 % Favored : 97.69 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3287 helix: 0.78 (0.17), residues: 934 sheet: -0.11 (0.19), residues: 688 loop : -0.07 (0.15), residues: 1665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 546 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 66 residues processed: 606 average time/residue: 1.9387 time to fit residues: 1562.1599 Evaluate side-chains 600 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 534 time to evaluate : 4.069 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 53 residues processed: 13 average time/residue: 1.1947 time to fit residues: 27.9296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 379 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 366 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 390 optimal weight: 7.9990 chunk 418 optimal weight: 30.0000 chunk 303 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 482 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS N 18 GLN P 75 GLN Q 72 ASN U 54 GLN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.089 102723 Z= 0.468 Angle : 0.923 20.089 154434 Z= 0.483 Chirality : 0.046 0.380 19724 Planarity : 0.010 0.164 7764 Dihedral : 13.943 178.275 41685 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.56 % Favored : 97.32 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 3287 helix: 0.54 (0.17), residues: 936 sheet: -0.19 (0.18), residues: 699 loop : -0.10 (0.15), residues: 1652 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 534 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 69 residues processed: 602 average time/residue: 1.9923 time to fit residues: 1601.4207 Evaluate side-chains 597 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 528 time to evaluate : 4.063 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 53 residues processed: 17 average time/residue: 1.1807 time to fit residues: 35.6509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 558 optimal weight: 1.9990 chunk 588 optimal weight: 3.9990 chunk 536 optimal weight: 5.9990 chunk 572 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 249 optimal weight: 0.9980 chunk 449 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 517 optimal weight: 1.9990 chunk 541 optimal weight: 5.9990 chunk 570 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS N 18 GLN P 75 GLN Q 72 ASN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 102723 Z= 0.199 Angle : 0.711 15.485 154434 Z= 0.399 Chirality : 0.036 0.372 19724 Planarity : 0.008 0.140 7764 Dihedral : 13.837 178.392 41685 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.22 % Favored : 97.66 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3287 helix: 0.79 (0.17), residues: 937 sheet: -0.11 (0.19), residues: 704 loop : -0.01 (0.15), residues: 1646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 532 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 63 residues processed: 589 average time/residue: 1.9600 time to fit residues: 1540.2845 Evaluate side-chains 596 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 533 time to evaluate : 3.982 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 52 residues processed: 11 average time/residue: 1.5974 time to fit residues: 28.9317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 375 optimal weight: 0.3980 chunk 605 optimal weight: 0.9990 chunk 369 optimal weight: 5.9990 chunk 287 optimal weight: 7.9990 chunk 420 optimal weight: 0.8980 chunk 634 optimal weight: 50.0000 chunk 584 optimal weight: 9.9990 chunk 505 optimal weight: 0.2980 chunk 52 optimal weight: 6.9990 chunk 390 optimal weight: 0.0470 chunk 309 optimal weight: 3.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS K 90 ASN N 18 GLN P 75 GLN Q 72 ASN Z 49 ASN d 28 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 102723 Z= 0.120 Angle : 0.671 13.650 154434 Z= 0.382 Chirality : 0.034 0.359 19724 Planarity : 0.008 0.133 7764 Dihedral : 13.869 177.308 41685 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.16 % Favored : 97.72 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3287 helix: 0.94 (0.17), residues: 935 sheet: -0.08 (0.19), residues: 698 loop : 0.02 (0.15), residues: 1654 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6574 Ramachandran restraints generated. 3287 Oldfield, 0 Emsley, 3287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 548 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 56 residues processed: 602 average time/residue: 1.9083 time to fit residues: 1542.9766 Evaluate side-chains 597 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 541 time to evaluate : 4.008 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 52 residues processed: 4 average time/residue: 0.7314 time to fit residues: 9.6562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 401 optimal weight: 10.0000 chunk 538 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 465 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 506 optimal weight: 0.9980 chunk 211 optimal weight: 100.0000 chunk 519 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 134 ASN K 29 HIS N 18 GLN P 75 GLN Q 72 ASN Z 49 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.176184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137852 restraints weight = 124494.981| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 0.45 r_work: 0.2993 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3954 r_free = 0.3954 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 102723 Z= 0.245 Angle : 0.737 16.305 154434 Z= 0.409 Chirality : 0.038 0.389 19724 Planarity : 0.008 0.146 7764 Dihedral : 13.798 178.933 41685 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.28 % Favored : 97.60 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3287 helix: 0.91 (0.17), residues: 933 sheet: -0.09 (0.19), residues: 704 loop : 0.04 (0.15), residues: 1650 =============================================================================== Job complete usr+sys time: 26857.87 seconds wall clock time: 471 minutes 43.01 seconds (28303.01 seconds total)