Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 16 17:55:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv1_14157/10_2023/7qv1_14157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv1_14157/10_2023/7qv1_14157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv1_14157/10_2023/7qv1_14157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv1_14157/10_2023/7qv1_14157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv1_14157/10_2023/7qv1_14157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv1_14157/10_2023/7qv1_14157.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.028 sd= 1.347 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4631 5.49 5 S 128 5.16 5 C 70228 2.51 5 N 26169 2.21 5 O 39618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 29": "OE1" <-> "OE2" Residue "1 GLU 11": "OE1" <-> "OE2" Residue "1 GLU 14": "OE1" <-> "OE2" Residue "1 ASP 28": "OD1" <-> "OD2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "6 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 23": "OE1" <-> "OE2" Residue "6 GLU 34": "OE1" <-> "OE2" Residue "6 TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 53": "OD1" <-> "OD2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "E TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ASP 14": "OD1" <-> "OD2" Residue "G ASP 21": "OD1" <-> "OD2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 99": "OE1" <-> "OE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 71": "NH1" <-> "NH2" Residue "L TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "N ARG 108": "NH1" <-> "NH2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "P ARG 14": "NH1" <-> "NH2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 93": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ASP 111": "OD1" <-> "OD2" Residue "R TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 63": "OE1" <-> "OE2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 75": "NH1" <-> "NH2" Residue "R ARG 89": "NH1" <-> "NH2" Residue "R GLU 98": "OE1" <-> "OE2" Residue "S TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 77": "OD1" <-> "OD2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T ASP 19": "OD1" <-> "OD2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T ASP 86": "OD1" <-> "OD2" Residue "T GLU 91": "OE1" <-> "OE2" Residue "U TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Z GLU 5": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "b GLU 13": "OE1" <-> "OE2" Residue "b GLU 31": "OE1" <-> "OE2" Residue "b GLU 39": "OE1" <-> "OE2" Residue "c TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 104": "OE1" <-> "OE2" Residue "c ASP 111": "OD1" <-> "OD2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 180": "OD1" <-> "OD2" Residue "c TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c GLU 205": "OE1" <-> "OE2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "d GLU 46": "OE1" <-> "OE2" Residue "d PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 91": "OD1" <-> "OD2" Residue "d ARG 146": "NH1" <-> "NH2" Residue "d TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 170": "OE1" <-> "OE2" Residue "d GLU 173": "OE1" <-> "OE2" Residue "d GLU 181": "OE1" <-> "OE2" Residue "d GLU 188": "OE1" <-> "OE2" Residue "e ARG 20": "NH1" <-> "NH2" Residue "e ARG 32": "NH1" <-> "NH2" Residue "e ASP 66": "OD1" <-> "OD2" Residue "e GLU 84": "OE1" <-> "OE2" Residue "e PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 112": "NH1" <-> "NH2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "f ARG 11": "NH1" <-> "NH2" Residue "f GLU 17": "OE1" <-> "OE2" Residue "f GLU 24": "OE1" <-> "OE2" Residue "f GLU 36": "OE1" <-> "OE2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 77": "NH1" <-> "NH2" Residue "f GLU 94": "OE1" <-> "OE2" Residue "g ASP 11": "OD1" <-> "OD2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g ARG 92": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "g TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 23": "OE1" <-> "OE2" Residue "h GLU 35": "OE1" <-> "OE2" Residue "h GLU 38": "OE1" <-> "OE2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 71": "OE1" <-> "OE2" Residue "h ARG 96": "NH1" <-> "NH2" Residue "h ASP 115": "OD1" <-> "OD2" Residue "h GLU 117": "OE1" <-> "OE2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "i ARG 12": "NH1" <-> "NH2" Residue "i ARG 20": "NH1" <-> "NH2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 9": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "j ASP 91": "OD1" <-> "OD2" Residue "j ASP 97": "OD1" <-> "OD2" Residue "k ARG 26": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l GLU 17": "OE1" <-> "OE2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "l TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 89": "OE1" <-> "OE2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 123": "NH1" <-> "NH2" Residue "m ARG 3": "NH1" <-> "NH2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m ARG 27": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 72": "OE1" <-> "OE2" Residue "m ARG 79": "NH1" <-> "NH2" Residue "m ARG 93": "NH1" <-> "NH2" Residue "n PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "o GLU 14": "OE1" <-> "OE2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ASP 74": "OD1" <-> "OD2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 19": "NH1" <-> "NH2" Residue "p ARG 29": "NH1" <-> "NH2" Residue "p ARG 32": "NH1" <-> "NH2" Residue "p PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 52": "OD1" <-> "OD2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "p ARG 71": "NH1" <-> "NH2" Residue "q ARG 39": "NH1" <-> "NH2" Residue "q ARG 67": "NH1" <-> "NH2" Residue "q GLU 79": "OE1" <-> "OE2" Residue "q GLU 83": "OE1" <-> "OE2" Residue "r PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 30": "OD1" <-> "OD2" Residue "r ASP 32": "OD1" <-> "OD2" Residue "r PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 48": "NH1" <-> "NH2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "t GLU 16": "OE1" <-> "OE2" Residue "t ARG 18": "NH1" <-> "NH2" Residue "t GLU 53": "OE1" <-> "OE2" Residue "t ARG 78": "NH1" <-> "NH2" Residue "u ARG 37": "NH1" <-> "NH2" Residue "u TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 38": "OE1" <-> "OE2" Residue "X GLU 70": "OE1" <-> "OE2" Residue "X ARG 88": "NH1" <-> "NH2" Residue "X GLU 136": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 140774 Number of models: 1 Model: "" Number of chains: 53 Chain: "0" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 499 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 52, 'rna3p_pyr': 43} Link IDs: {'rna2p': 17, 'rna3p': 94} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "F" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "H" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 2, 'TRANS': 21} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "M" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "P" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 944 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "U" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "V" Number of atoms: 61998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2887, 61998 Inner-chain residues flagged as termini: ['pdbres=" G V 328 "', 'pdbres=" G V1220 "'] Classifications: {'RNA': 2887} Modifications used: {'5*END': 3, 'rna2p_pur': 306, 'rna2p_pyr': 161, 'rna3p_pur': 1372, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 467, 'rna3p': 2419} Chain breaks: 3 Chain: "W" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "a" Number of atoms: 32891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32891 Classifications: {'RNA': 1533} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 88, 'rna3p_pur': 752, 'rna3p_pyr': 575} Link IDs: {'rna2p': 205, 'rna3p': 1327} Chain: "b" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 476 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "c" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 3, 'TRANS': 202} Chain: "d" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1568 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "e" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1218 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "f" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "g" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1203 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "h" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1036 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "j" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "k" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 871 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "l" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "m" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 740 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "n" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 497 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "p" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "r" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "s" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 624 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "t" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "u" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "X" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1151 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "A" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 559 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna2p': 6, 'rna3p': 19} Time building chain proxies: 51.61, per 1000 atoms: 0.37 Number of scatterers: 140774 At special positions: 0 Unit cell: (272.85, 272.85, 260.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 P 4631 15.00 O 39618 8.00 N 26169 7.00 C 70228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS n 24 " - pdb=" SG CYS n 40 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 60.49 Conformation dependent library (CDL) restraints added in 5.1 seconds 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9662 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 69 sheets defined 36.1% alpha, 18.4% beta 1511 base pairs and 2332 stacking pairs defined. Time for finding SS restraints: 47.75 Creating SS restraints... Processing helix chain '0' and resid 9 through 18 Processing helix chain '0' and resid 19 through 21 No H-bonds generated for 'chain '0' and resid 19 through 21' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 3.684A pdb=" N SER 2 24 " --> pdb=" O SER 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain '3' and resid 7 through 12 Processing helix chain '3' and resid 18 through 20 No H-bonds generated for 'chain '3' and resid 18 through 20' Processing helix chain '3' and resid 32 through 36 Processing helix chain '3' and resid 37 through 45 Processing helix chain '3' and resid 51 through 59 Processing helix chain '3' and resid 60 through 62 No H-bonds generated for 'chain '3' and resid 60 through 62' Processing helix chain '4' and resid 18 through 22 Processing helix chain '4' and resid 29 through 32 Processing helix chain '6' and resid 40 through 45 removed outlier: 3.657A pdb=" N GLY 6 45 " --> pdb=" O PHE 6 42 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 54 Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.714A pdb=" N ARG C 14 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.904A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.042A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 62 through 71 removed outlier: 4.066A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.819A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 29 through 45 Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.800A pdb=" N VAL E 57 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 Processing helix chain 'E' and resid 135 through 146 removed outlier: 4.048A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.534A pdb=" N VAL E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'F' and resid 4 through 21 removed outlier: 4.701A pdb=" N ALA F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.925A pdb=" N VAL F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 removed outlier: 3.654A pdb=" N ILE F 50 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 61 removed outlier: 3.534A pdb=" N PHE F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 3.532A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 111 Processing helix chain 'F' and resid 138 through 142 removed outlier: 3.527A pdb=" N ASP F 142 " --> pdb=" O PRO F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.535A pdb=" N ALA F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.710A pdb=" N ALA G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.625A pdb=" N ALA G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 39 removed outlier: 3.963A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 90 through 96 Processing helix chain 'J' and resid 97 through 110 Processing helix chain 'J' and resid 113 through 121 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'K' and resid 104 through 109 removed outlier: 3.792A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.922A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.649A pdb=" N ARG L 41 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 61 Processing helix chain 'L' and resid 80 through 85 Processing helix chain 'L' and resid 92 through 100 Processing helix chain 'L' and resid 129 through 140 Processing helix chain 'M' and resid 44 through 59 Processing helix chain 'M' and resid 110 through 123 Processing helix chain 'N' and resid 9 through 28 Processing helix chain 'N' and resid 34 through 54 removed outlier: 4.301A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 Processing helix chain 'N' and resid 79 through 92 Processing helix chain 'O' and resid 6 through 20 removed outlier: 3.715A pdb=" N ALA O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 88 Processing helix chain 'O' and resid 104 through 117 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 11 through 13 No H-bonds generated for 'chain 'P' and resid 11 through 13' Processing helix chain 'P' and resid 53 through 56 Processing helix chain 'P' and resid 97 through 102 removed outlier: 3.754A pdb=" N LEU P 100 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.743A pdb=" N ARG Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 Processing helix chain 'Q' and resid 31 through 73 removed outlier: 4.367A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.919A pdb=" N GLY Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 102 Processing helix chain 'Q' and resid 105 through 116 Processing helix chain 'S' and resid 13 through 22 Processing helix chain 'S' and resid 28 through 37 Processing helix chain 'S' and resid 43 through 62 Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'S' and resid 88 through 92 removed outlier: 3.825A pdb=" N GLY S 91 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 6 Processing helix chain 'T' and resid 14 through 22 removed outlier: 3.769A pdb=" N THR T 22 " --> pdb=" O ALA T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 48 Processing helix chain 'U' and resid 50 through 54 removed outlier: 4.591A pdb=" N GLN U 53 " --> pdb=" O ALA U 50 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY U 54 " --> pdb=" O ASN U 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 50 through 54' Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 12 through 35 Processing helix chain 'Y' and resid 40 through 65 removed outlier: 4.156A pdb=" N ARG Y 44 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE Y 57 " --> pdb=" O MET Y 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 25 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'b' and resid 11 through 23 removed outlier: 3.950A pdb=" N ALA b 15 " --> pdb=" O SER b 11 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU b 16 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG b 18 " --> pdb=" O ASP b 14 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 26 No H-bonds generated for 'chain 'b' and resid 24 through 26' Processing helix chain 'b' and resid 30 through 35 removed outlier: 4.105A pdb=" N ARG b 35 " --> pdb=" O GLU b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 55 removed outlier: 3.948A pdb=" N LYS b 48 " --> pdb=" O LYS b 44 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER b 49 " --> pdb=" O ARG b 45 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG b 53 " --> pdb=" O SER b 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 Processing helix chain 'c' and resid 71 through 75 Processing helix chain 'c' and resid 79 through 95 removed outlier: 3.511A pdb=" N VAL c 83 " --> pdb=" O GLY c 79 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA c 89 " --> pdb=" O ALA c 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU c 90 " --> pdb=" O LEU c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 Processing helix chain 'c' and resid 130 through 144 Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 45 through 62 Processing helix chain 'd' and resid 64 through 78 Processing helix chain 'd' and resid 81 through 91 removed outlier: 3.707A pdb=" N MET d 87 " --> pdb=" O GLY d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 106 through 116 Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'd' and resid 181 through 186 removed outlier: 3.635A pdb=" N ALA d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 193 through 200 Processing helix chain 'e' and resid 55 through 69 removed outlier: 3.574A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 76 through 80 Processing helix chain 'e' and resid 108 through 118 Processing helix chain 'e' and resid 132 through 146 Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'e' and resid 160 through 166 Processing helix chain 'f' and resid 15 through 31 Processing helix chain 'f' and resid 70 through 82 Processing helix chain 'g' and resid 20 through 29 Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.622A pdb=" N SER g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.683A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 4.247A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 129 Processing helix chain 'g' and resid 132 through 148 Processing helix chain 'g' and resid 149 through 152 Processing helix chain 'h' and resid 6 through 21 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 115 through 122 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 42 through 49 removed outlier: 3.599A pdb=" N GLU i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS i 49 " --> pdb=" O ILE i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 55 Processing helix chain 'i' and resid 71 through 91 Processing helix chain 'i' and resid 94 through 99 Processing helix chain 'j' and resid 14 through 31 Processing helix chain 'j' and resid 80 through 89 Processing helix chain 'k' and resid 49 through 53 Processing helix chain 'k' and resid 56 through 60 Processing helix chain 'k' and resid 61 through 80 removed outlier: 4.550A pdb=" N GLU k 78 " --> pdb=" O LYS k 74 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS k 79 " --> pdb=" O GLY k 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 105 removed outlier: 4.549A pdb=" N ALA k 97 " --> pdb=" O SER k 93 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE k 99 " --> pdb=" O ARG k 95 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Processing helix chain 'l' and resid 21 through 25 removed outlier: 3.572A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 25' Processing helix chain 'l' and resid 128 through 132 removed outlier: 4.095A pdb=" N THR l 132 " --> pdb=" O LYS l 129 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 21 removed outlier: 3.578A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 63 Processing helix chain 'm' and resid 65 through 83 removed outlier: 4.102A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'n' and resid 3 through 12 Processing helix chain 'n' and resid 16 through 20 Processing helix chain 'n' and resid 40 through 50 Processing helix chain 'o' and resid 6 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.613A pdb=" N HIS o 42 " --> pdb=" O ASN o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 74 through 86 Processing helix chain 'p' and resid 52 through 63 Processing helix chain 'p' and resid 67 through 77 removed outlier: 3.807A pdb=" N LEU p 73 " --> pdb=" O THR p 69 " (cutoff:3.500A) Processing helix chain 'p' and resid 78 through 89 Processing helix chain 'r' and resid 16 through 22 removed outlier: 3.616A pdb=" N SER r 20 " --> pdb=" O CYS r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 38 Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 70 Processing helix chain 's' and resid 12 through 24 Processing helix chain 's' and resid 41 through 45 Processing helix chain 's' and resid 63 through 69 removed outlier: 3.860A pdb=" N GLY s 68 " --> pdb=" O ASP s 65 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 Processing helix chain 't' and resid 7 through 41 Processing helix chain 't' and resid 44 through 65 Processing helix chain 't' and resid 68 through 85 Processing helix chain 'u' and resid 51 through 55 Processing helix chain 'X' and resid 22 through 34 Processing helix chain 'X' and resid 40 through 74 removed outlier: 4.132A pdb=" N LEU X 68 " --> pdb=" O GLN X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 88 removed outlier: 3.522A pdb=" N GLY X 87 " --> pdb=" O GLY X 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG X 88 " --> pdb=" O GLU X 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 84 through 88' Processing helix chain 'X' and resid 94 through 105 Processing sheet with id=AA1, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain '0' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain '1' and resid 17 through 22 removed outlier: 3.572A pdb=" N LYS 1 41 " --> pdb=" O CYS 1 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 15 through 16 Processing sheet with id=AA5, first strand: chain '4' and resid 2 through 3 removed outlier: 5.671A pdb=" N LYS 4 2 " --> pdb=" O LYS 4 35 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN 4 34 " --> pdb=" O VAL 4 25 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL 4 25 " --> pdb=" O GLN 4 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '6' and resid 21 through 26 removed outlier: 4.186A pdb=" N VAL 6 31 " --> pdb=" O THR 6 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.510A pdb=" N ARG C 102 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 16 removed outlier: 6.610A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE D 188 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU D 175 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 173 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AB4, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.558A pdb=" N ILE D 49 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 118 through 120 removed outlier: 3.594A pdb=" N GLY D 162 " --> pdb=" O GLN D 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 14 removed outlier: 4.536A pdb=" N LEU E 6 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 88 through 91 removed outlier: 3.529A pdb=" N LYS F 33 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.602A pdb=" N LEU G 9 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 50 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA G 54 " --> pdb=" O GLU G 43 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU G 43 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 16 through 19 Processing sheet with id=AC1, first strand: chain 'G' and resid 123 through 125 removed outlier: 3.660A pdb=" N VAL G 91 " --> pdb=" O GLY G 162 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY G 162 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 96 through 100 Processing sheet with id=AC3, first strand: chain 'J' and resid 123 through 125 removed outlier: 6.554A pdb=" N TRP J 16 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=AC5, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.591A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL K 19 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR K 21 " --> pdb=" O CYS K 41 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS K 41 " --> pdb=" O THR K 21 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N CYS K 84 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE K 86 " --> pdb=" O LYS K 9 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.517A pdb=" N ILE K 77 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE P 64 " --> pdb=" O GLU P 44 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N GLU P 44 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR P 25 " --> pdb=" O VAL P 86 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL P 86 " --> pdb=" O THR P 25 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ARG P 27 " --> pdb=" O ILE P 84 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE P 84 " --> pdb=" O ARG P 27 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N HIS P 29 " --> pdb=" O ALA P 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 102 through 103 removed outlier: 6.503A pdb=" N VAL K 102 " --> pdb=" O ILE K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'L' and resid 75 through 77 removed outlier: 5.586A pdb=" N ALA L 75 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL L 109 " --> pdb=" O LYS L 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'L' and resid 90 through 91 removed outlier: 5.862A pdb=" N VAL L 91 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 102 through 106 removed outlier: 6.655A pdb=" N VAL M 102 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA M 36 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 40 through 43 removed outlier: 3.700A pdb=" N SER M 40 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL M 97 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY M 92 " --> pdb=" O TYR M 74 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.242A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 70 through 72 removed outlier: 7.378A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 32 through 35 removed outlier: 3.697A pdb=" N ALA O 54 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP O 46 " --> pdb=" O THR O 52 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR O 52 " --> pdb=" O ASP O 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.708A pdb=" N ILE R 5 " --> pdb=" O ILE R 12 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 32 through 35 Processing sheet with id=AD8, first strand: chain 'R' and resid 65 through 67 Processing sheet with id=AD9, first strand: chain 'R' and resid 71 through 76 Processing sheet with id=AE1, first strand: chain 'S' and resid 3 through 6 removed outlier: 6.740A pdb=" N SER S 108 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AE3, first strand: chain 'T' and resid 8 through 11 removed outlier: 3.584A pdb=" N ARG T 10 " --> pdb=" O GLU T 29 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS T 53 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 62 through 64 removed outlier: 3.559A pdb=" N ALA U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 40 through 42 Processing sheet with id=AE6, first strand: chain 'U' and resid 81 through 85 removed outlier: 3.552A pdb=" N LYS U 84 " --> pdb=" O VAL U 91 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 30 through 31 removed outlier: 6.775A pdb=" N LEU W 67 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE W 68 " --> pdb=" O GLY W 60 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY W 60 " --> pdb=" O PHE W 68 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 38 through 39 removed outlier: 6.712A pdb=" N TYR W 54 " --> pdb=" O VAL W 87 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N VAL W 89 " --> pdb=" O TYR W 54 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 35 through 38 Processing sheet with id=AF1, first strand: chain 'c' and resid 20 through 21 removed outlier: 3.742A pdb=" N LYS c 21 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG c 58 " --> pdb=" O LYS c 21 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL c 63 " --> pdb=" O HIS c 99 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN c 101 " --> pdb=" O VAL c 63 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE c 65 " --> pdb=" O ASN c 101 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE c 67 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 165 through 170 removed outlier: 3.689A pdb=" N VAL c 152 " --> pdb=" O GLU c 165 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR c 167 " --> pdb=" O THR c 150 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 139 through 140 removed outlier: 3.684A pdb=" N THR d 166 " --> pdb=" O THR d 175 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 14 through 24 removed outlier: 5.040A pdb=" N LEU e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL e 38 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'e' and resid 85 through 88 Processing sheet with id=AF6, first strand: chain 'f' and resid 36 through 47 removed outlier: 6.746A pdb=" N ILE f 37 " --> pdb=" O GLN f 66 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLN f 66 " --> pdb=" O ILE f 37 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY f 39 " --> pdb=" O ASN f 64 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS f 45 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLY f 58 " --> pdb=" O LYS f 45 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG f 87 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 73 through 78 Processing sheet with id=AF8, first strand: chain 'h' and resid 46 through 52 removed outlier: 4.061A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 76 through 78 removed outlier: 3.829A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 76 through 78 removed outlier: 3.829A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'i' and resid 6 through 9 removed outlier: 3.533A pdb=" N ARG i 20 " --> pdb=" O LEU i 64 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU i 64 " --> pdb=" O ARG i 20 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL i 22 " --> pdb=" O ASP i 62 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'j' and resid 7 through 12 Processing sheet with id=AG4, first strand: chain 'j' and resid 40 through 41 Processing sheet with id=AG5, first strand: chain 'k' and resid 43 through 48 Processing sheet with id=AG6, first strand: chain 'l' and resid 26 through 29 Processing sheet with id=AG7, first strand: chain 'l' and resid 42 through 53 removed outlier: 5.941A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR l 108 " --> pdb=" O THR l 77 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE l 110 " --> pdb=" O TYR l 79 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'p' and resid 3 through 11 removed outlier: 3.509A pdb=" N ALA p 23 " --> pdb=" O LYS p 4 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE p 20 " --> pdb=" O VAL p 37 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'q' and resid 9 through 19 removed outlier: 7.200A pdb=" N THR q 24 " --> pdb=" O VAL q 15 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP q 17 " --> pdb=" O THR q 22 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR q 22 " --> pdb=" O ASP q 17 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ARG q 74 " --> pdb=" O LYS q 45 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LYS q 47 " --> pdb=" O ARG q 74 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG q 76 " --> pdb=" O LYS q 47 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N HIS q 49 " --> pdb=" O ARG q 76 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL q 78 " --> pdb=" O HIS q 49 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ARG q 74 " --> pdb=" O THR q 66 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE q 60 " --> pdb=" O VAL q 80 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'q' and resid 31 through 32 removed outlier: 3.506A pdb=" N LYS q 31 " --> pdb=" O VAL q 40 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 's' and resid 32 through 33 removed outlier: 8.499A pdb=" N THR s 33 " --> pdb=" O TYR s 52 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'u' and resid 13 through 18 removed outlier: 3.893A pdb=" N SER u 25 " --> pdb=" O ASN u 17 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'u' and resid 33 through 36 removed outlier: 3.555A pdb=" N VAL u 36 " --> pdb=" O VAL u 47 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'X' and resid 19 through 20 removed outlier: 4.175A pdb=" N LYS X 19 " --> pdb=" O VAL X 3 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL X 3 " --> pdb=" O LYS X 19 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 79 through 80 removed outlier: 3.665A pdb=" N ALA X 139 " --> pdb=" O VAL X 131 " (cutoff:3.500A) 1667 hydrogen bonds defined for protein. 4662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3843 hydrogen bonds 6218 hydrogen bond angles 0 basepair planarities 1511 basepair parallelities 2332 stacking parallelities Total time for adding SS restraints: 210.87 Time building geometry restraints manager: 65.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 23143 1.33 - 1.45: 64004 1.45 - 1.58: 56610 1.58 - 1.70: 9256 1.70 - 1.82: 231 Bond restraints: 153244 Sorted by residual: bond pdb=" C1' C A 41 " pdb=" N1 C A 41 " ideal model delta sigma weight residual 1.480 1.562 -0.082 1.50e-02 4.44e+03 2.98e+01 bond pdb=" C1' A A 42 " pdb=" N9 A A 42 " ideal model delta sigma weight residual 1.475 1.395 0.080 1.50e-02 4.44e+03 2.88e+01 bond pdb=" C1' U A 39 " pdb=" N1 U A 39 " ideal model delta sigma weight residual 1.470 1.550 -0.080 1.50e-02 4.44e+03 2.86e+01 bond pdb=" C1' C A 50 " pdb=" N1 C A 50 " ideal model delta sigma weight residual 1.480 1.558 -0.078 1.50e-02 4.44e+03 2.72e+01 bond pdb=" C1' U A 32 " pdb=" N1 U A 32 " ideal model delta sigma weight residual 1.480 1.552 -0.072 1.50e-02 4.44e+03 2.33e+01 ... (remaining 153239 not shown) Histogram of bond angle deviations from ideal: 18.69 - 41.74: 1 41.74 - 64.80: 0 64.80 - 87.86: 0 87.86 - 110.91: 87194 110.91 - 133.97: 142639 Bond angle restraints: 229834 Sorted by residual: angle pdb=" O3' U V 138 " pdb=" P A V 139 " pdb=" OP1 A V 139 " ideal model delta sigma weight residual 108.00 18.69 89.31 3.00e+00 1.11e-01 8.86e+02 angle pdb=" C3' U A 32 " pdb=" O3' U A 32 " pdb=" P A A 33 " ideal model delta sigma weight residual 120.20 108.67 11.53 1.50e+00 4.44e-01 5.91e+01 angle pdb=" C3' C V1449 " pdb=" O3' C V1449 " pdb=" P C V1450 " ideal model delta sigma weight residual 120.20 109.74 10.46 1.50e+00 4.44e-01 4.86e+01 angle pdb=" C3' G A 37 " pdb=" O3' G A 37 " pdb=" P A A 38 " ideal model delta sigma weight residual 120.20 109.82 10.38 1.50e+00 4.44e-01 4.79e+01 angle pdb=" C3' C V1450 " pdb=" O3' C V1450 " pdb=" P U V1451 " ideal model delta sigma weight residual 120.20 109.89 10.31 1.50e+00 4.44e-01 4.72e+01 ... (remaining 229829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 78637 35.98 - 71.95: 2644 71.95 - 107.93: 265 107.93 - 143.91: 67 143.91 - 179.88: 59 Dihedral angle restraints: 81672 sinusoidal: 66653 harmonic: 15019 Sorted by residual: dihedral pdb=" C4' G V2009 " pdb=" C3' G V2009 " pdb=" C2' G V2009 " pdb=" C1' G V2009 " ideal model delta sinusoidal sigma weight residual -35.00 36.05 -71.05 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C5' G V2009 " pdb=" C4' G V2009 " pdb=" C3' G V2009 " pdb=" O3' G V2009 " ideal model delta sinusoidal sigma weight residual 147.00 78.69 68.31 1 8.00e+00 1.56e-02 9.46e+01 dihedral pdb=" O4' C V2231 " pdb=" C1' C V2231 " pdb=" N1 C V2231 " pdb=" C2 C V2231 " ideal model delta sinusoidal sigma weight residual 200.00 34.96 165.04 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 81669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 29045 0.104 - 0.209: 375 0.209 - 0.313: 6 0.313 - 0.417: 25 0.417 - 0.521: 12 Chirality restraints: 29463 Sorted by residual: chirality pdb=" P A V 139 " pdb=" OP1 A V 139 " pdb=" OP2 A V 139 " pdb=" O5' A V 139 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" P U V 420 " pdb=" OP1 U V 420 " pdb=" OP2 U V 420 " pdb=" O5' U V 420 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" P U V1448 " pdb=" OP1 U V1448 " pdb=" OP2 U V1448 " pdb=" O5' U V1448 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 29460 not shown) Planarity restraints: 11836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G V2122 " -0.051 2.00e-02 2.50e+03 2.09e-02 1.32e+01 pdb=" N9 G V2122 " 0.046 2.00e-02 2.50e+03 pdb=" C8 G V2122 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G V2122 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G V2122 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G V2122 " -0.011 2.00e-02 2.50e+03 pdb=" O6 G V2122 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G V2122 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G V2122 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G V2122 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G V2122 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G V2122 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C V 509 " 0.008 2.00e-02 2.50e+03 2.37e-02 1.26e+01 pdb=" N1 C V 509 " -0.005 2.00e-02 2.50e+03 pdb=" C2 C V 509 " -0.058 2.00e-02 2.50e+03 pdb=" O2 C V 509 " 0.034 2.00e-02 2.50e+03 pdb=" N3 C V 509 " 0.006 2.00e-02 2.50e+03 pdb=" C4 C V 509 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C V 509 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C V 509 " 0.009 2.00e-02 2.50e+03 pdb=" C6 C V 509 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 117 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LYS D 117 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS D 117 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY D 118 " -0.019 2.00e-02 2.50e+03 ... (remaining 11833 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 277 2.24 - 2.91: 49947 2.91 - 3.57: 223701 3.57 - 4.24: 422838 4.24 - 4.90: 576808 Nonbonded interactions: 1273571 Sorted by model distance: nonbonded pdb=" OP1 C a 817 " pdb=" CE LYS o 48 " model vdw 1.575 3.440 nonbonded pdb=" O2' A a 474 " pdb=" O5' A a 475 " model vdw 1.866 2.440 nonbonded pdb=" O2' U a1461 " pdb=" OP1 U a1462 " model vdw 1.876 2.440 nonbonded pdb=" OP1 U a 413 " pdb=" O2' G a 414 " model vdw 1.876 2.440 nonbonded pdb=" O2' A a 209 " pdb=" O4' A a 210 " model vdw 1.890 2.440 ... (remaining 1273566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 15.930 Check model and map are aligned: 1.540 Set scattering table: 0.960 Process input model: 464.800 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 490.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.002 0.082 153244 Z= 0.128 Angle : 0.509 89.315 229834 Z= 0.269 Chirality : 0.033 0.521 29463 Planarity : 0.002 0.033 11836 Dihedral : 15.472 179.885 72007 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 0.41 % Allowed : 4.84 % Favored : 94.75 % Cbeta Deviations : 0.00 % 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: -2.06 (0.11), residues: 5160 helix: -0.16 (0.12), residues: 1671 sheet: -1.42 (0.16), residues: 967 loop : -2.19 (0.11), residues: 2522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1991 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1973 time to evaluate : 6.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 1983 average time/residue: 1.2914 time to fit residues: 4341.8291 Evaluate side-chains 1353 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1351 time to evaluate : 5.987 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.0124 time to fit residues: 9.9704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 816 optimal weight: 5.9990 chunk 732 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 chunk 494 optimal weight: 10.0000 chunk 391 optimal weight: 20.0000 chunk 757 optimal weight: 30.0000 chunk 293 optimal weight: 10.0000 chunk 460 optimal weight: 10.0000 chunk 564 optimal weight: 20.0000 chunk 878 optimal weight: 0.0570 overall best weight: 7.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 25 ASN 6 20 ASN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 200 HIS ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN E 46 GLN ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 GLN K 4 GLN M 13 HIS N 27 ASN N 61 GLN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS O 64 ASN ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN S 57 ASN T 35 ASN U 39 ASN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 159 ASN e 135 ASN ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 GLN k 24 HIS k 121 ASN l 6 GLN l 85 HIS n 10 GLN o 51 HIS o 83 ASN ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 85 ASN p 88 GLN r 53 ASN s 29 GLN t 68 HIS u 16 ASN X 28 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 153244 Z= 0.377 Angle : 0.746 11.026 229834 Z= 0.378 Chirality : 0.040 0.329 29463 Planarity : 0.006 0.096 11836 Dihedral : 15.954 178.963 61406 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.36 % Favored : 92.54 % Rotamer: Outliers : 5.61 % Allowed : 17.56 % Favored : 76.82 % Cbeta Deviations : 0.00 % 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: -1.46 (0.11), residues: 5160 helix: 0.31 (0.12), residues: 1661 sheet: -1.10 (0.16), residues: 977 loop : -1.80 (0.12), residues: 2522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1748 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1501 time to evaluate : 5.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 247 outliers final: 161 residues processed: 1607 average time/residue: 1.2612 time to fit residues: 3522.5855 Evaluate side-chains 1422 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1261 time to evaluate : 7.503 Switching outliers to nearest non-outliers outliers start: 161 outliers final: 0 residues processed: 161 average time/residue: 1.0679 time to fit residues: 334.4019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 488 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 730 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 879 optimal weight: 20.0000 chunk 950 optimal weight: 0.9990 chunk 783 optimal weight: 5.9990 chunk 872 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 705 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 16 ASN C 200 HIS ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 HIS K 4 GLN N 27 ASN ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN S 95 GLN T 35 ASN Y 4 ASN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 84 ASN ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 HIS ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 121 ASN l 6 GLN l 88 GLN ** p 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 ASN ** X 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 153244 Z= 0.254 Angle : 0.615 15.560 229834 Z= 0.315 Chirality : 0.036 0.290 29463 Planarity : 0.005 0.067 11836 Dihedral : 15.771 179.744 61406 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.40 % Favored : 93.57 % Rotamer: Outliers : 3.41 % Allowed : 21.02 % Favored : 75.57 % Cbeta Deviations : 0.00 % 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: -1.11 (0.11), residues: 5160 helix: 0.66 (0.13), residues: 1659 sheet: -0.81 (0.16), residues: 966 loop : -1.68 (0.11), residues: 2535 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1381 time to evaluate : 6.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 73 residues processed: 1448 average time/residue: 1.2401 time to fit residues: 3120.8340 Evaluate side-chains 1327 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1254 time to evaluate : 6.118 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 1.0705 time to fit residues: 151.5660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 869 optimal weight: 20.0000 chunk 661 optimal weight: 20.0000 chunk 456 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 419 optimal weight: 10.0000 chunk 590 optimal weight: 10.0000 chunk 882 optimal weight: 9.9990 chunk 934 optimal weight: 40.0000 chunk 461 optimal weight: 10.0000 chunk 836 optimal weight: 2.9990 chunk 251 optimal weight: 7.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 26 HIS ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 153 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS L 78 ASN L 83 ASN ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN S 37 ASN U 59 GLN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 64 ASN g 19 ASN ** g 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 ASN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS l 6 GLN l 86 ASN l 109 HIS n 19 GLN r 53 ASN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 ASN ** X 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 153244 Z= 0.418 Angle : 0.752 14.059 229834 Z= 0.382 Chirality : 0.042 0.329 29463 Planarity : 0.006 0.084 11836 Dihedral : 16.284 179.778 61406 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.26 % Favored : 91.69 % Rotamer: Outliers : 4.54 % Allowed : 23.36 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.11), residues: 5160 helix: 0.46 (0.12), residues: 1659 sheet: -0.92 (0.16), residues: 984 loop : -1.71 (0.12), residues: 2517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1511 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1311 time to evaluate : 6.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 200 outliers final: 117 residues processed: 1388 average time/residue: 1.2395 time to fit residues: 2984.8844 Evaluate side-chains 1313 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1196 time to evaluate : 6.049 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 0 residues processed: 117 average time/residue: 0.9966 time to fit residues: 228.2718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 778 optimal weight: 5.9990 chunk 530 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 695 optimal weight: 50.0000 chunk 385 optimal weight: 5.9990 chunk 797 optimal weight: 5.9990 chunk 646 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 477 optimal weight: 10.0000 chunk 838 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 6 HIS ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS G 23 ASN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 HIS K 3 GLN L 78 ASN L 106 ASN ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN O 43 GLN Q 38 GLN Q 91 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN S 95 GLN ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 40 GLN ** g 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 ASN ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN n 19 GLN ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 153244 Z= 0.206 Angle : 0.603 12.703 229834 Z= 0.311 Chirality : 0.035 0.282 29463 Planarity : 0.004 0.055 11836 Dihedral : 15.886 179.509 61406 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.51 % Favored : 93.45 % Rotamer: Outliers : 2.45 % Allowed : 25.43 % Favored : 72.12 % Cbeta Deviations : 0.00 % 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: -1.06 (0.11), residues: 5160 helix: 0.63 (0.13), residues: 1675 sheet: -0.72 (0.17), residues: 931 loop : -1.62 (0.12), residues: 2554 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1331 time to evaluate : 6.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 58 residues processed: 1374 average time/residue: 1.2192 time to fit residues: 2924.2494 Evaluate side-chains 1289 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1231 time to evaluate : 6.006 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.9861 time to fit residues: 113.5960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 314 optimal weight: 30.0000 chunk 841 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 548 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 935 optimal weight: 40.0000 chunk 776 optimal weight: 3.9990 chunk 433 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 491 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 55 ASN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN Q 38 GLN Q 72 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 95 GLN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 121 ASN l 6 GLN ** X 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 153244 Z= 0.375 Angle : 0.707 13.095 229834 Z= 0.361 Chirality : 0.040 0.321 29463 Planarity : 0.005 0.084 11836 Dihedral : 16.189 179.667 61406 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.22 % Favored : 91.72 % Rotamer: Outliers : 3.34 % Allowed : 27.15 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 5160 helix: 0.43 (0.13), residues: 1659 sheet: -0.83 (0.17), residues: 956 loop : -1.65 (0.12), residues: 2545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1400 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1253 time to evaluate : 6.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 98 residues processed: 1312 average time/residue: 1.2030 time to fit residues: 2747.2539 Evaluate side-chains 1292 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1194 time to evaluate : 5.459 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 0.9415 time to fit residues: 181.3970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 902 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 533 optimal weight: 10.0000 chunk 683 optimal weight: 8.9990 chunk 529 optimal weight: 6.9990 chunk 787 optimal weight: 8.9990 chunk 522 optimal weight: 10.0000 chunk 932 optimal weight: 5.9990 chunk 583 optimal weight: 1.9990 chunk 568 optimal weight: 10.0000 chunk 430 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN G 129 GLN J 131 HIS ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 95 GLN ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 34 GLN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 153244 Z= 0.318 Angle : 0.672 12.262 229834 Z= 0.345 Chirality : 0.039 0.314 29463 Planarity : 0.005 0.089 11836 Dihedral : 16.127 179.806 61406 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.44 % Rotamer: Outliers : 2.02 % Allowed : 28.61 % Favored : 69.37 % Cbeta Deviations : 0.00 % 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: -1.20 (0.11), residues: 5160 helix: 0.43 (0.13), residues: 1656 sheet: -0.79 (0.17), residues: 968 loop : -1.62 (0.12), residues: 2536 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1272 time to evaluate : 6.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 48 residues processed: 1312 average time/residue: 1.2139 time to fit residues: 2775.8615 Evaluate side-chains 1261 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1213 time to evaluate : 6.001 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 1.0453 time to fit residues: 99.8891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 576 optimal weight: 6.9990 chunk 372 optimal weight: 10.0000 chunk 556 optimal weight: 10.0000 chunk 280 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 180 optimal weight: 0.8980 chunk 592 optimal weight: 6.9990 chunk 634 optimal weight: 20.0000 chunk 460 optimal weight: 10.0000 chunk 86 optimal weight: 40.0000 chunk 732 optimal weight: 10.0000 overall best weight: 6.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 ASN C 226 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 75 GLN F 172 GLN ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN l 25 ASN l 86 ASN u 23 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 153244 Z= 0.369 Angle : 0.723 13.507 229834 Z= 0.370 Chirality : 0.041 0.321 29463 Planarity : 0.005 0.094 11836 Dihedral : 16.310 179.920 61406 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.53 % Favored : 91.40 % Rotamer: Outliers : 2.41 % Allowed : 29.58 % Favored : 68.01 % Cbeta Deviations : 0.00 % 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: -1.35 (0.11), residues: 5160 helix: 0.18 (0.12), residues: 1665 sheet: -0.80 (0.17), residues: 972 loop : -1.68 (0.12), residues: 2523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1248 time to evaluate : 6.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 80 residues processed: 1278 average time/residue: 1.3121 time to fit residues: 2927.6788 Evaluate side-chains 1281 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1201 time to evaluate : 5.699 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.9866 time to fit residues: 156.3347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 847 optimal weight: 4.9990 chunk 892 optimal weight: 10.0000 chunk 814 optimal weight: 9.9990 chunk 868 optimal weight: 0.3980 chunk 522 optimal weight: 10.0000 chunk 378 optimal weight: 30.0000 chunk 682 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 784 optimal weight: 0.9990 chunk 821 optimal weight: 8.9990 chunk 865 optimal weight: 6.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 HIS N 27 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 43 ASN ** X 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 153244 Z= 0.240 Angle : 0.643 13.552 229834 Z= 0.332 Chirality : 0.037 0.294 29463 Planarity : 0.005 0.095 11836 Dihedral : 16.055 179.711 61406 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.67 % Rotamer: Outliers : 0.95 % Allowed : 30.63 % Favored : 68.42 % Cbeta Deviations : 0.00 % 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: -1.25 (0.11), residues: 5160 helix: 0.26 (0.12), residues: 1663 sheet: -0.68 (0.17), residues: 949 loop : -1.62 (0.12), residues: 2548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1255 time to evaluate : 6.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 25 residues processed: 1273 average time/residue: 1.2301 time to fit residues: 2732.7215 Evaluate side-chains 1223 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1198 time to evaluate : 6.055 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.9848 time to fit residues: 53.6362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 570 optimal weight: 10.0000 chunk 918 optimal weight: 8.9990 chunk 560 optimal weight: 20.0000 chunk 435 optimal weight: 20.0000 chunk 638 optimal weight: 20.0000 chunk 963 optimal weight: 0.0050 chunk 886 optimal weight: 0.0970 chunk 767 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 592 optimal weight: 7.9990 chunk 470 optimal weight: 10.0000 overall best weight: 5.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 HIS ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Q 72 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 95 GLN ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 ASN ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 43 ASN ** X 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 153244 Z= 0.300 Angle : 0.684 15.191 229834 Z= 0.352 Chirality : 0.038 0.302 29463 Planarity : 0.005 0.082 11836 Dihedral : 16.145 179.868 61406 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.26 % Favored : 91.69 % Rotamer: Outliers : 0.89 % Allowed : 32.24 % Favored : 66.87 % Cbeta Deviations : 0.00 % 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: -1.32 (0.11), residues: 5160 helix: 0.12 (0.12), residues: 1663 sheet: -0.71 (0.17), residues: 961 loop : -1.62 (0.12), residues: 2536 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1270 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1231 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 31 residues processed: 1241 average time/residue: 1.2317 time to fit residues: 2674.9033 Evaluate side-chains 1234 residues out of total 4401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1203 time to evaluate : 6.114 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 1.0161 time to fit residues: 65.9979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 609 optimal weight: 10.0000 chunk 817 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 707 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 213 optimal weight: 0.0070 chunk 768 optimal weight: 0.6980 chunk 321 optimal weight: 10.0000 chunk 788 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 141 optimal weight: 30.0000 overall best weight: 3.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN ** l 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 43 ASN ** X 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.082999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.059519 restraints weight = 501781.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.061096 restraints weight = 215049.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060771 restraints weight = 120493.315| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 153244 Z= 0.203 Angle : 0.626 15.538 229834 Z= 0.323 Chirality : 0.035 0.272 29463 Planarity : 0.005 0.092 11836 Dihedral : 15.920 179.466 61406 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.21 % Favored : 92.73 % Rotamer: Outliers : 0.57 % Allowed : 32.47 % Favored : 66.96 % Cbeta Deviations : 0.00 % 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: -1.20 (0.11), residues: 5160 helix: 0.21 (0.13), residues: 1654 sheet: -0.52 (0.17), residues: 917 loop : -1.57 (0.12), residues: 2589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39691.33 seconds wall clock time: 691 minutes 42.91 seconds (41502.91 seconds total)