Starting phenix.real_space_refine on Tue Mar 19 07:04:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/03_2024/7bl6_12219_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/03_2024/7bl6_12219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/03_2024/7bl6_12219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/03_2024/7bl6_12219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/03_2024/7bl6_12219_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl6_12219/03_2024/7bl6_12219_updated.pdb" } resolution = 4.0 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= 0.034 sd= 0.170 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3018 5.49 5 Mg 2 5.21 5 S 94 5.16 5 C 46425 2.51 5 N 17251 2.21 5 O 25977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "g ARG 24": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ASP 52": "OD1" <-> "OD2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 67": "OD1" <-> "OD2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ASP 109": "OD1" <-> "OD2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 56": "OE1" <-> "OE2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 7": "NH1" <-> "NH2" Residue "W ASP 52": "OD1" <-> "OD2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ASP 49": "OD1" <-> "OD2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ASP 39": "OD1" <-> "OD2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ASP 19": "OD1" <-> "OD2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 5": "NH1" <-> "NH2" Residue "1 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P GLU 26": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 60": "NH1" <-> "NH2" Residue "9 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 66": "NH1" <-> "NH2" Residue "9 ARG 114": "NH1" <-> "NH2" Residue "9 ARG 139": "NH1" <-> "NH2" Residue "9 ARG 150": "NH1" <-> "NH2" Residue "9 GLU 155": "OE1" <-> "OE2" Residue "9 ASP 161": "OD1" <-> "OD2" Residue "9 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 177": "NH1" <-> "NH2" Residue "9 TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 230": "NH1" <-> "NH2" Residue "9 PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 239": "NH1" <-> "NH2" Residue "9 ARG 278": "NH1" <-> "NH2" Residue "9 TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 92769 Number of models: 1 Model: "" Number of chains: 42 Chain: "g" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1483 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 1 Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 577 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "P" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 144} Chain: "d" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 364 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "A" Number of atoms: 62195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 273, 'rna2p_pyr': 144, 'rna3p_pur': 1399, 'rna3p_pyr': 1081} Link IDs: {'rna2p': 417, 'rna3p': 2479} Chain breaks: 1 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2548 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2582 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 85 SG CYS g 11 67.792 178.993 66.710 1.00277.97 S ATOM 110 SG CYS g 14 70.774 177.662 68.668 1.00281.13 S ATOM 213 SG CYS g 27 69.296 181.145 69.478 1.00293.05 S ATOM 24643 SG CYS d 16 21.903 84.234 28.463 1.00436.92 S ATOM 24797 SG CYS d 37 23.738 87.221 26.891 1.00411.36 S Time building chain proxies: 36.91, per 1000 atoms: 0.40 Number of scatterers: 92769 At special positions: 0 Unit cell: (180.96, 233.16, 234.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 94 16.00 P 3018 15.00 Mg 2 11.99 O 25977 8.00 N 17251 7.00 C 46425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 44.64 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN d 100 " pdb="ZN ZN d 100 " - pdb=" SG CYS d 37 " pdb="ZN ZN d 100 " - pdb=" SG CYS d 16 " pdb=" ZN g 101 " pdb="ZN ZN g 101 " - pdb=" ND1 HIS g 33 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 11 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 27 " pdb="ZN ZN g 101 " - pdb=" SG CYS g 14 " Number of angles added : 3 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 101 helices and 48 sheets defined 24.2% alpha, 17.6% beta 979 base pairs and 1519 stacking pairs defined. Time for finding SS restraints: 43.34 Creating SS restraints... Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 62 through 71 removed outlier: 3.603A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 121 through 125 Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 25 through 39 Processing helix chain 'E' and resid 98 through 114 Processing helix chain 'E' and resid 131 through 140 Processing helix chain 'E' and resid 155 through 162 Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.980A pdb=" N LYS F 8 " --> pdb=" O HIS F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 Processing helix chain 'F' and resid 24 through 26 No H-bonds generated for 'chain 'F' and resid 24 through 26' Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 47 through 59 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 60 through 79 removed outlier: 3.960A pdb=" N GLY G 65 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL G 75 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR G 79 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.877A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 removed outlier: 3.837A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 99 through 108 removed outlier: 3.688A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY J 107 " --> pdb=" O ILE J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.799A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 70 through 73 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.925A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 68 Processing helix chain 'N' and resid 73 through 78 Processing helix chain 'N' and resid 83 through 88 Processing helix chain 'O' and resid 4 through 20 removed outlier: 4.494A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 85 Processing helix chain 'O' and resid 102 through 113 Processing helix chain 'Q' and resid 8 through 19 Processing helix chain 'Q' and resid 25 through 28 Processing helix chain 'Q' and resid 31 through 70 removed outlier: 4.440A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 91 through 100 Processing helix chain 'Q' and resid 102 through 116 Processing helix chain 'S' and resid 14 through 23 removed outlier: 3.623A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 37 removed outlier: 3.761A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 60 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 4 through 10 Processing helix chain 'T' and resid 18 through 25 Processing helix chain 'T' and resid 40 through 50 Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'V' and resid 14 through 22 Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'V' and resid 54 through 57 removed outlier: 3.963A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 54 through 57' Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 63 through 72 Processing helix chain 'Y' and resid 10 through 21 Processing helix chain 'Y' and resid 25 through 33 Processing helix chain 'Y' and resid 40 through 55 removed outlier: 3.525A pdb=" N LYS Y 44 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG Y 48 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR Y 55 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 49 Processing helix chain '0' and resid 9 through 19 removed outlier: 3.713A pdb=" N SER 0 17 " --> pdb=" O GLY 0 13 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 Processing helix chain '2' and resid 18 through 22 Processing helix chain '2' and resid 25 through 37 Processing helix chain 'K' and resid 105 through 109 Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'P' and resid 3 through 11 removed outlier: 4.352A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 97 through 100 removed outlier: 3.539A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 100' Processing helix chain 'M' and resid 43 through 56 Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.896A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 26 No H-bonds generated for 'chain 'H' and resid 23 through 26' Processing helix chain 'H' and resid 43 through 46 No H-bonds generated for 'chain 'H' and resid 43 through 46' Processing helix chain 'H' and resid 48 through 51 removed outlier: 3.588A pdb=" N ARG H 51 " --> pdb=" O GLU H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 51' Processing helix chain 'H' and resid 54 through 74 removed outlier: 4.096A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain '9' and resid 57 through 59 No H-bonds generated for 'chain '9' and resid 57 through 59' Processing helix chain '9' and resid 127 through 130 Processing helix chain '9' and resid 172 through 179 removed outlier: 3.691A pdb=" N ILE 9 176 " --> pdb=" O LYS 9 172 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG 9 177 " --> pdb=" O SER 9 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA 9 178 " --> pdb=" O THR 9 174 " (cutoff:3.500A) Processing helix chain '9' and resid 230 through 233 Processing helix chain '9' and resid 255 through 268 removed outlier: 3.989A pdb=" N ARG 9 260 " --> pdb=" O VAL 9 256 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE 9 262 " --> pdb=" O ASN 9 258 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE 9 263 " --> pdb=" O ALA 9 259 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER 9 264 " --> pdb=" O ARG 9 260 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU 9 265 " --> pdb=" O ILE 9 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS 9 268 " --> pdb=" O SER 9 264 " (cutoff:3.500A) Processing helix chain '9' and resid 272 through 275 Processing helix chain '9' and resid 285 through 287 No H-bonds generated for 'chain '9' and resid 285 through 287' Processing helix chain '9' and resid 291 through 304 removed outlier: 3.503A pdb=" N GLU 9 294 " --> pdb=" O VAL 9 291 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU 9 295 " --> pdb=" O GLU 9 292 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS 9 296 " --> pdb=" O ALA 9 293 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE 9 300 " --> pdb=" O ALA 9 297 " (cutoff:3.500A) Processing helix chain '9' and resid 321 through 334 removed outlier: 3.859A pdb=" N TRP 9 326 " --> pdb=" O LYS 9 322 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU 9 334 " --> pdb=" O THR 9 330 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 12 removed outlier: 3.612A pdb=" N ARG 3 12 " --> pdb=" O GLY 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 34 No H-bonds generated for 'chain '3' and resid 32 through 34' Processing helix chain '3' and resid 37 through 44 removed outlier: 3.635A pdb=" N ARG 3 44 " --> pdb=" O LYS 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 60 Processing sheet with id= A, first strand: chain 'g' and resid 14 through 19 Processing sheet with id= B, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= C, first strand: chain 'C' and resid 114 through 117 removed outlier: 4.340A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.966A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 169 through 172 removed outlier: 4.582A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.072A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 117 through 119 Processing sheet with id= I, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.939A pdb=" N VAL E 186 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL E 121 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET E 188 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 126 through 130 removed outlier: 6.812A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 22 through 24 Processing sheet with id= L, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.792A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 160 through 163 Processing sheet with id= N, first strand: chain 'G' and resid 93 through 98 removed outlier: 3.510A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 138 through 140 removed outlier: 4.957A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR J 53 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL J 18 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= Q, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.667A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.855A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.649A pdb=" N GLY N 101 " --> pdb=" O MET N 110 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR N 112 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS N 99 " --> pdb=" O TYR N 112 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLU N 114 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE N 97 " --> pdb=" O GLU N 114 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 25 through 30 Processing sheet with id= U, first strand: chain 'R' and resid 40 through 42 removed outlier: 3.733A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'R' and resid 20 through 23 removed outlier: 4.157A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'R' and resid 32 through 35 removed outlier: 3.929A pdb=" N VAL R 58 " --> pdb=" O SER R 102 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER R 102 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS R 60 " --> pdb=" O GLY R 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY R 100 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.143A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'S' and resid 3 through 7 removed outlier: 6.271A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'S' and resid 81 through 87 Processing sheet with id= AA, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.673A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'T' and resid 67 through 69 Processing sheet with id= AC, first strand: chain 'U' and resid 69 through 71 removed outlier: 4.176A pdb=" N ASP U 8 " --> pdb=" O VAL U 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL U 24 " --> pdb=" O ASP U 8 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'U' and resid 40 through 44 Processing sheet with id= AE, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AF, first strand: chain 'V' and resid 3 through 6 removed outlier: 6.879A pdb=" N THR V 62 " --> pdb=" O ILE V 4 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA V 6 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL V 64 " --> pdb=" O ALA V 6 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'W' and resid 47 through 49 Processing sheet with id= AH, first strand: chain 'W' and resid 62 through 68 Processing sheet with id= AI, first strand: chain 'X' and resid 12 through 15 Processing sheet with id= AJ, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.559A pdb=" N VAL X 39 " --> pdb=" O ARG X 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.516A pdb=" N ILE Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '1' and resid 19 through 24 removed outlier: 3.634A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 6 through 9 removed outlier: 6.964A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.601A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE P 58 " --> pdb=" O PHE P 73 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 128 through 132 removed outlier: 6.316A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU M 104 " --> pdb=" O TRP M 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP M 64 " --> pdb=" O GLU M 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP M 106 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 39 through 42 removed outlier: 4.183A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE M 96 " --> pdb=" O GLY M 39 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'M' and resid 72 through 74 removed outlier: 3.874A pdb=" N TYR M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 78 through 83 Processing sheet with id= AS, first strand: chain 'd' and resid 11 through 15 removed outlier: 3.912A pdb=" N ILE d 24 " --> pdb=" O ILE d 12 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA d 14 " --> pdb=" O MET d 22 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain '9' and resid 64 through 66 removed outlier: 8.737A pdb=" N PHE 9 65 " --> pdb=" O SER 9 8 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU 9 10 " --> pdb=" O PHE 9 65 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '9' and resid 45 through 50 removed outlier: 5.875A pdb=" N VAL 9 86 " --> pdb=" O TRP 9 46 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU 9 48 " --> pdb=" O VAL 9 86 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE 9 88 " --> pdb=" O GLU 9 48 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP 9 50 " --> pdb=" O ILE 9 88 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL 9 90 " --> pdb=" O ASP 9 50 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain '9' and resid 162 through 166 removed outlier: 6.482A pdb=" N VAL 9 240 " --> pdb=" O GLY 9 163 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU 9 165 " --> pdb=" O VAL 9 240 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU 9 242 " --> pdb=" O LEU 9 165 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL 9 281 " --> pdb=" O ILE 9 245 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV 760 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2492 hydrogen bonds 3934 hydrogen bond angles 0 basepair planarities 979 basepair parallelities 1519 stacking parallelities Total time for adding SS restraints: 134.57 Time building geometry restraints manager: 47.77 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: 15888 1.33 - 1.46: 41822 1.46 - 1.58: 36978 1.58 - 1.70: 6032 1.70 - 1.82: 168 Bond restraints: 100888 Sorted by residual: bond pdb=" N3B GNP 9 402 " pdb=" PG GNP 9 402 " ideal model delta sigma weight residual 1.801 1.709 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O5' GNP 9 402 " pdb=" PA GNP 9 402 " ideal model delta sigma weight residual 1.660 1.574 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CA LYS 9 31 " pdb=" CB LYS 9 31 " ideal model delta sigma weight residual 1.528 1.587 -0.059 2.61e-02 1.47e+03 5.07e+00 bond pdb=" O3A GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.687 1.643 0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" N3B GNP 9 402 " pdb=" PB GNP 9 402 " ideal model delta sigma weight residual 1.681 1.639 0.042 2.00e-02 2.50e+03 4.49e+00 ... (remaining 100883 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.25: 14040 105.25 - 112.43: 58162 112.43 - 119.61: 32275 119.61 - 126.79: 38356 126.79 - 133.97: 8345 Bond angle restraints: 151178 Sorted by residual: angle pdb=" N GLU Q 110 " pdb=" CA GLU Q 110 " pdb=" CB GLU Q 110 " ideal model delta sigma weight residual 110.28 118.17 -7.89 1.55e+00 4.16e-01 2.59e+01 angle pdb=" CB ARG Y 23 " pdb=" CG ARG Y 23 " pdb=" CD ARG Y 23 " ideal model delta sigma weight residual 111.30 122.83 -11.53 2.30e+00 1.89e-01 2.51e+01 angle pdb=" C VAL Q 109 " pdb=" N GLU Q 110 " pdb=" CA GLU Q 110 " ideal model delta sigma weight residual 120.31 112.96 7.35 1.52e+00 4.33e-01 2.34e+01 angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 129.07 -7.37 1.80e+00 3.09e-01 1.68e+01 angle pdb=" CA GLU Q 110 " pdb=" CB GLU Q 110 " pdb=" CG GLU Q 110 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.59e+01 ... (remaining 151173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 56709 35.66 - 71.33: 7028 71.33 - 106.99: 799 106.99 - 142.66: 5 142.66 - 178.32: 10 Dihedral angle restraints: 64551 sinusoidal: 54370 harmonic: 10181 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 53.66 146.34 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" O4' U A1061 " pdb=" C1' U A1061 " pdb=" N1 U A1061 " pdb=" C2 U A1061 " ideal model delta sinusoidal sigma weight residual -128.00 50.32 -178.32 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 50.31 -178.31 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 64548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 18341 0.054 - 0.109: 888 0.109 - 0.163: 114 0.163 - 0.218: 7 0.218 - 0.272: 1 Chirality restraints: 19351 Sorted by residual: chirality pdb=" C1' U A1736 " pdb=" O4' U A1736 " pdb=" C2' U A1736 " pdb=" N1 U A1736 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' G A2505 " pdb=" C4' G A2505 " pdb=" O3' G A2505 " pdb=" C2' G A2505 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ARG Y 23 " pdb=" N ARG Y 23 " pdb=" C ARG Y 23 " pdb=" CB ARG Y 23 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 19348 not shown) Planarity restraints: 7924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A1736 " -0.031 2.00e-02 2.50e+03 1.69e-02 6.41e+00 pdb=" N1 U A1736 " 0.038 2.00e-02 2.50e+03 pdb=" C2 U A1736 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U A1736 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U A1736 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A1736 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U A1736 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U A1736 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U A1736 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 643 " -0.029 2.00e-02 2.50e+03 1.33e-02 4.90e+00 pdb=" N9 A A 643 " 0.031 2.00e-02 2.50e+03 pdb=" C8 A A 643 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 643 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 643 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A 643 " -0.000 2.00e-02 2.50e+03 pdb=" N6 A A 643 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A A 643 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 643 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 643 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A A 643 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 100 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C ASN G 100 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN G 100 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL G 101 " 0.012 2.00e-02 2.50e+03 ... (remaining 7921 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 5251 2.67 - 3.23: 81646 3.23 - 3.79: 191011 3.79 - 4.34: 245200 4.34 - 4.90: 323028 Nonbonded interactions: 846136 Sorted by model distance: nonbonded pdb="MG MG 9 401 " pdb=" O2G GNP 9 402 " model vdw 2.117 2.170 nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 2.126 2.440 nonbonded pdb=" O2' C A2258 " pdb=" OP2 C A2427 " model vdw 2.130 2.440 nonbonded pdb=" OG1 THR O 31 " pdb=" O HIS O 34 " model vdw 2.154 2.440 nonbonded pdb=" N2 G A1171 " pdb=" O2 C A1178 " model vdw 2.157 2.496 ... (remaining 846131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 7.300 Check model and map are aligned: 1.220 Set scattering table: 0.700 Process input model: 334.310 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 348.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 0.092 100888 Z= 0.098 Angle : 0.423 11.526 151178 Z= 0.226 Chirality : 0.025 0.272 19351 Planarity : 0.003 0.052 7924 Dihedral : 22.700 178.319 58003 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 0.07 % Allowed : 0.31 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.28 (0.14), residues: 3538 helix: 0.52 (0.18), residues: 858 sheet: 0.89 (0.21), residues: 672 loop : -0.89 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 212 HIS 0.007 0.001 HIS M 13 PHE 0.038 0.001 PHE H 46 TYR 0.022 0.001 TYR F 127 ARG 0.006 0.000 ARG Y 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 4.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 1 MET cc_start: 0.7085 (ppp) cc_final: 0.6603 (ppp) REVERT: D 39 ASP cc_start: 0.9272 (p0) cc_final: 0.9028 (p0) REVERT: E 188 MET cc_start: 0.8921 (tpt) cc_final: 0.8491 (tpp) REVERT: F 2 LYS cc_start: 0.9775 (mmpt) cc_final: 0.9562 (tptt) REVERT: F 137 PHE cc_start: 0.8774 (m-10) cc_final: 0.8514 (m-80) REVERT: G 38 ASP cc_start: 0.9252 (m-30) cc_final: 0.8918 (t0) REVERT: G 115 GLN cc_start: 0.9269 (tp40) cc_final: 0.8884 (tp-100) REVERT: J 108 MET cc_start: 0.8795 (mmp) cc_final: 0.8459 (mmm) REVERT: L 55 MET cc_start: 0.9128 (tpt) cc_final: 0.8517 (tpp) REVERT: N 20 MET cc_start: 0.9277 (ppp) cc_final: 0.8792 (ppp) REVERT: N 110 MET cc_start: 0.9065 (mmp) cc_final: 0.8166 (mmm) REVERT: R 1 MET cc_start: 0.8584 (tpt) cc_final: 0.8185 (tmm) REVERT: V 48 MET cc_start: 0.9220 (mpp) cc_final: 0.8756 (mpp) REVERT: Y 15 ASN cc_start: 0.9246 (m110) cc_final: 0.8961 (m110) REVERT: P 12 MET cc_start: 0.8513 (mmp) cc_final: 0.7830 (mmm) REVERT: M 12 MET cc_start: 0.8977 (tpt) cc_final: 0.8650 (tpp) REVERT: M 82 MET cc_start: 0.9044 (mmp) cc_final: 0.8373 (mmm) REVERT: M 105 MET cc_start: 0.8342 (mmm) cc_final: 0.7643 (mmm) REVERT: d 22 MET cc_start: 0.8814 (pmm) cc_final: 0.8523 (pmm) REVERT: 9 108 MET cc_start: 0.8799 (mmp) cc_final: 0.8371 (mmm) REVERT: 9 203 MET cc_start: 0.9201 (pmm) cc_final: 0.8899 (pmm) REVERT: 9 310 TYR cc_start: 0.9431 (p90) cc_final: 0.9217 (p90) outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.8501 time to fit residues: 235.6434 Evaluate side-chains 132 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 60 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 545 optimal weight: 40.0000 chunk 489 optimal weight: 40.0000 chunk 271 optimal weight: 0.0170 chunk 167 optimal weight: 4.9990 chunk 330 optimal weight: 30.0000 chunk 261 optimal weight: 40.0000 chunk 506 optimal weight: 30.0000 chunk 195 optimal weight: 50.0000 chunk 307 optimal weight: 30.0000 chunk 376 optimal weight: 40.0000 chunk 586 optimal weight: 40.0000 overall best weight: 19.0032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 126 ASN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 135 GLN N 11 ASN S 7 HIS S 31 GLN T 59 ASN U 68 ASN V 49 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN K 3 GLN H 18 GLN 9 99 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.132 100888 Z= 0.458 Angle : 0.784 16.032 151178 Z= 0.389 Chirality : 0.038 0.337 19351 Planarity : 0.006 0.135 7924 Dihedral : 23.727 178.855 51018 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 34.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.09 % Rotamer: Outliers : 0.69 % Allowed : 7.95 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.61 (0.14), residues: 3538 helix: 0.15 (0.18), residues: 890 sheet: 0.26 (0.19), residues: 739 loop : -0.92 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP X 38 HIS 0.011 0.002 HIS Q 13 PHE 0.034 0.003 PHE Z 52 TYR 0.024 0.002 TYR V 57 ARG 0.030 0.001 ARG g 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 4.030 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: g 1 MET cc_start: 0.8105 (ppp) cc_final: 0.7456 (ppp) REVERT: F 137 PHE cc_start: 0.9098 (m-10) cc_final: 0.8801 (m-10) REVERT: G 38 ASP cc_start: 0.9458 (m-30) cc_final: 0.9139 (t0) REVERT: J 92 MET cc_start: 0.9548 (mmm) cc_final: 0.8533 (tpp) REVERT: L 55 MET cc_start: 0.9525 (tpt) cc_final: 0.8618 (tpt) REVERT: N 20 MET cc_start: 0.9408 (ppp) cc_final: 0.8858 (ppp) REVERT: N 24 MET cc_start: 0.9591 (mmt) cc_final: 0.9016 (mmt) REVERT: N 110 MET cc_start: 0.9156 (mmp) cc_final: 0.8296 (mmm) REVERT: V 48 MET cc_start: 0.9059 (mpp) cc_final: 0.8721 (mpp) REVERT: Y 1 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.9034 (tmm) REVERT: Y 15 ASN cc_start: 0.9198 (m110) cc_final: 0.8847 (m110) REVERT: Z 2 LYS cc_start: 0.7991 (tmtt) cc_final: 0.7752 (tmtt) REVERT: Z 46 MET cc_start: 0.9378 (mmp) cc_final: 0.9152 (mmm) REVERT: M 1 MET cc_start: 0.8132 (tmm) cc_final: 0.7931 (ppp) REVERT: M 82 MET cc_start: 0.9200 (mmp) cc_final: 0.8426 (mmm) REVERT: M 105 MET cc_start: 0.8858 (mmm) cc_final: 0.8434 (mmm) REVERT: M 136 MET cc_start: 0.6770 (ppp) cc_final: 0.6128 (pmm) REVERT: 9 108 MET cc_start: 0.9500 (mmp) cc_final: 0.9204 (mmm) REVERT: 9 310 TYR cc_start: 0.9610 (p90) cc_final: 0.9380 (p90) outliers start: 20 outliers final: 9 residues processed: 157 average time/residue: 0.8452 time to fit residues: 236.5767 Evaluate side-chains 140 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 44 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 326 optimal weight: 30.0000 chunk 182 optimal weight: 9.9990 chunk 488 optimal weight: 20.0000 chunk 399 optimal weight: 30.0000 chunk 161 optimal weight: 30.0000 chunk 587 optimal weight: 30.0000 chunk 634 optimal weight: 20.0000 chunk 523 optimal weight: 50.0000 chunk 582 optimal weight: 30.0000 chunk 200 optimal weight: 40.0000 chunk 471 optimal weight: 30.0000 overall best weight: 21.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 13 ASN ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 67 HIS D 164 GLN D 185 ASN E 41 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 20 ASN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN L 104 GLN N 107 ASN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN Y 25 GLN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 145 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.280 100888 Z= 0.449 Angle : 0.786 20.933 151178 Z= 0.396 Chirality : 0.041 0.360 19351 Planarity : 0.006 0.065 7924 Dihedral : 24.522 175.695 51015 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 43.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.42 % Favored : 93.41 % Rotamer: Outliers : 1.95 % Allowed : 12.30 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.13), residues: 3538 helix: -0.42 (0.17), residues: 895 sheet: -0.23 (0.19), residues: 747 loop : -1.26 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP X 38 HIS 0.013 0.002 HIS R 89 PHE 0.034 0.003 PHE H 29 TYR 0.030 0.003 TYR K 32 ARG 0.016 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 134 time to evaluate : 4.098 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: g 1 MET cc_start: 0.8069 (ppp) cc_final: 0.7615 (ppp) REVERT: C 153 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9413 (mm) REVERT: C 180 MET cc_start: 0.9041 (mmm) cc_final: 0.8722 (mmm) REVERT: D 48 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9147 (mm) REVERT: F 137 PHE cc_start: 0.9232 (m-10) cc_final: 0.8940 (m-10) REVERT: G 80 GLU cc_start: 0.9351 (tm-30) cc_final: 0.8910 (pm20) REVERT: J 80 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8216 (t-170) REVERT: J 92 MET cc_start: 0.9600 (mmm) cc_final: 0.9184 (tpt) REVERT: J 108 MET cc_start: 0.9615 (mmp) cc_final: 0.9246 (mmp) REVERT: J 118 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8623 (tpp) REVERT: L 55 MET cc_start: 0.9426 (tpt) cc_final: 0.9016 (tpp) REVERT: N 20 MET cc_start: 0.9597 (ppp) cc_final: 0.9302 (tmm) REVERT: N 24 MET cc_start: 0.9638 (mmt) cc_final: 0.9232 (mmt) REVERT: N 110 MET cc_start: 0.9170 (mmp) cc_final: 0.8581 (mmm) REVERT: S 1 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8617 (ppp) REVERT: S 109 ASP cc_start: 0.9707 (p0) cc_final: 0.9441 (p0) REVERT: T 1 MET cc_start: 0.7625 (mtm) cc_final: 0.6900 (mpp) REVERT: V 48 MET cc_start: 0.8819 (mpp) cc_final: 0.8505 (mpp) REVERT: Y 7 ARG cc_start: 0.9517 (ptt90) cc_final: 0.8924 (ptt-90) REVERT: Z 46 MET cc_start: 0.9397 (mmp) cc_final: 0.9029 (mmm) REVERT: 2 1 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8476 (ppp) REVERT: K 20 MET cc_start: 0.9363 (tpp) cc_final: 0.8921 (tpp) REVERT: M 82 MET cc_start: 0.9129 (mmp) cc_final: 0.8353 (mmm) REVERT: M 105 MET cc_start: 0.9015 (mmm) cc_final: 0.8644 (mmm) REVERT: H 1 MET cc_start: 0.9276 (ppp) cc_final: 0.9028 (ppp) REVERT: H 75 LEU cc_start: 0.8018 (mt) cc_final: 0.7721 (pp) REVERT: H 136 SER cc_start: 0.9428 (OUTLIER) cc_final: 0.9204 (p) REVERT: d 1 MET cc_start: 0.9463 (tpp) cc_final: 0.8613 (tpp) REVERT: 9 108 MET cc_start: 0.9382 (mmp) cc_final: 0.8946 (mmm) REVERT: 9 157 MET cc_start: 0.8065 (tpt) cc_final: 0.6971 (tpp) outliers start: 57 outliers final: 24 residues processed: 178 average time/residue: 0.9322 time to fit residues: 300.0955 Evaluate side-chains 152 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 11 CYS Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain O residue 84 GLU Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain 9 residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 580 optimal weight: 30.0000 chunk 441 optimal weight: 20.0000 chunk 305 optimal weight: 50.0000 chunk 65 optimal weight: 8.9990 chunk 280 optimal weight: 7.9990 chunk 394 optimal weight: 30.0000 chunk 589 optimal weight: 30.0000 chunk 624 optimal weight: 10.0000 chunk 308 optimal weight: 30.0000 chunk 558 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 13 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 100888 Z= 0.249 Angle : 0.577 12.104 151178 Z= 0.294 Chirality : 0.033 0.331 19351 Planarity : 0.004 0.043 7924 Dihedral : 24.328 178.408 51015 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 28.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 1.85 % Allowed : 14.29 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -0.91 (0.14), residues: 3538 helix: 0.11 (0.18), residues: 890 sheet: -0.16 (0.19), residues: 727 loop : -1.11 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 212 HIS 0.006 0.001 HIS O 34 PHE 0.023 0.002 PHE H 29 TYR 0.019 0.001 TYR F 127 ARG 0.005 0.000 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 128 time to evaluate : 4.095 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: g 1 MET cc_start: 0.8143 (ppp) cc_final: 0.7866 (ppp) REVERT: E 1 MET cc_start: 0.8972 (pmm) cc_final: 0.8590 (pmm) REVERT: F 37 MET cc_start: 0.9292 (mmm) cc_final: 0.8929 (mmm) REVERT: F 137 PHE cc_start: 0.9247 (m-10) cc_final: 0.8939 (m-10) REVERT: G 80 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8929 (pp20) REVERT: J 80 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8224 (t-90) REVERT: J 92 MET cc_start: 0.9585 (mmm) cc_final: 0.9122 (tpt) REVERT: J 108 MET cc_start: 0.9522 (mmp) cc_final: 0.9315 (mmp) REVERT: L 55 MET cc_start: 0.9258 (tpt) cc_final: 0.8717 (tpt) REVERT: N 20 MET cc_start: 0.9592 (ppp) cc_final: 0.9102 (ppp) REVERT: N 24 MET cc_start: 0.9647 (mmt) cc_final: 0.9183 (mmt) REVERT: N 110 MET cc_start: 0.9078 (mmp) cc_final: 0.8505 (mmm) REVERT: N 120 GLU cc_start: 0.8225 (pm20) cc_final: 0.7962 (pm20) REVERT: O 76 LYS cc_start: 0.9749 (pttm) cc_final: 0.9537 (pttp) REVERT: T 1 MET cc_start: 0.8054 (mtm) cc_final: 0.7755 (mpp) REVERT: Z 46 MET cc_start: 0.9506 (mmp) cc_final: 0.9003 (mmm) REVERT: K 7 MET cc_start: 0.9207 (tpt) cc_final: 0.8864 (tpt) REVERT: K 20 MET cc_start: 0.9329 (tpp) cc_final: 0.9124 (tpp) REVERT: M 12 MET cc_start: 0.9401 (mmm) cc_final: 0.9064 (tpp) REVERT: M 82 MET cc_start: 0.9207 (mmp) cc_final: 0.8517 (mmm) REVERT: M 105 MET cc_start: 0.8494 (mmm) cc_final: 0.8147 (mmm) REVERT: H 75 LEU cc_start: 0.8419 (mt) cc_final: 0.8144 (pp) REVERT: H 136 SER cc_start: 0.9429 (m) cc_final: 0.9204 (p) REVERT: d 1 MET cc_start: 0.8529 (tpp) cc_final: 0.7995 (tpp) REVERT: d 3 LYS cc_start: 0.9390 (mmtt) cc_final: 0.9125 (mmtt) REVERT: 9 108 MET cc_start: 0.9382 (mmp) cc_final: 0.9035 (mmm) REVERT: 9 157 MET cc_start: 0.8049 (tpt) cc_final: 0.6749 (tpt) REVERT: 9 310 TYR cc_start: 0.8952 (p90) cc_final: 0.8637 (p90) outliers start: 54 outliers final: 22 residues processed: 172 average time/residue: 0.9088 time to fit residues: 280.9690 Evaluate side-chains 146 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 19 ASN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain 9 residue 237 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 520 optimal weight: 50.0000 chunk 354 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 464 optimal weight: 40.0000 chunk 257 optimal weight: 9.9990 chunk 532 optimal weight: 40.0000 chunk 431 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 318 optimal weight: 30.0000 chunk 560 optimal weight: 30.0000 chunk 157 optimal weight: 20.0000 overall best weight: 23.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN G 29 ASN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN 1 18 HIS ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** d 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 100888 Z= 0.506 Angle : 0.815 12.873 151178 Z= 0.406 Chirality : 0.041 0.341 19351 Planarity : 0.006 0.052 7924 Dihedral : 24.696 177.145 51015 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 49.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.17 % Favored : 91.75 % Rotamer: Outliers : 2.71 % Allowed : 15.35 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.37 (0.14), residues: 3538 helix: -0.31 (0.17), residues: 875 sheet: -0.64 (0.19), residues: 755 loop : -1.28 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP M 92 HIS 0.010 0.002 HIS O 34 PHE 0.033 0.003 PHE H 29 TYR 0.018 0.002 TYR F 142 ARG 0.018 0.001 ARG d 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 122 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8184 (p) REVERT: D 48 ILE cc_start: 0.9570 (OUTLIER) cc_final: 0.9149 (mm) REVERT: F 137 PHE cc_start: 0.9340 (m-10) cc_final: 0.9045 (m-10) REVERT: G 148 ARG cc_start: 0.9718 (OUTLIER) cc_final: 0.9322 (ptm160) REVERT: J 80 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.8225 (t-170) REVERT: J 92 MET cc_start: 0.9623 (mmm) cc_final: 0.8981 (tpt) REVERT: J 108 MET cc_start: 0.9535 (mmp) cc_final: 0.9030 (mmp) REVERT: L 55 MET cc_start: 0.9425 (tpt) cc_final: 0.9069 (tpp) REVERT: N 20 MET cc_start: 0.9668 (ppp) cc_final: 0.9295 (ppp) REVERT: N 24 MET cc_start: 0.9641 (mmt) cc_final: 0.9235 (mmt) REVERT: N 110 MET cc_start: 0.9035 (mmp) cc_final: 0.8585 (mmm) REVERT: S 1 MET cc_start: 0.8910 (ppp) cc_final: 0.8678 (ppp) REVERT: Z 46 MET cc_start: 0.9570 (mmp) cc_final: 0.9079 (mmm) REVERT: K 7 MET cc_start: 0.9081 (tpt) cc_final: 0.8869 (tpt) REVERT: M 82 MET cc_start: 0.9070 (mmp) cc_final: 0.8285 (mmm) REVERT: M 105 MET cc_start: 0.8834 (mmm) cc_final: 0.8534 (mmm) REVERT: 9 157 MET cc_start: 0.7971 (tpt) cc_final: 0.6925 (tpp) REVERT: 9 310 TYR cc_start: 0.8757 (p90) cc_final: 0.8507 (p90) outliers start: 79 outliers final: 39 residues processed: 192 average time/residue: 0.8298 time to fit residues: 286.2906 Evaluate side-chains 159 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 116 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 11 CYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain O residue 84 GLU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 237 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 210 optimal weight: 10.0000 chunk 562 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 366 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 625 optimal weight: 0.0010 chunk 518 optimal weight: 50.0000 chunk 289 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 overall best weight: 14.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 6 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 100888 Z= 0.294 Angle : 0.632 14.170 151178 Z= 0.321 Chirality : 0.035 0.397 19351 Planarity : 0.005 0.044 7924 Dihedral : 24.669 176.483 51015 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 35.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.76 % Favored : 93.19 % Rotamer: Outliers : 2.54 % Allowed : 16.90 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.23 (0.14), residues: 3538 helix: -0.11 (0.18), residues: 891 sheet: -0.67 (0.19), residues: 744 loop : -1.18 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 212 HIS 0.007 0.001 HIS O 34 PHE 0.033 0.002 PHE H 29 TYR 0.017 0.002 TYR F 127 ARG 0.005 0.001 ARG 9 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 121 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8296 (p) REVERT: D 48 ILE cc_start: 0.9573 (OUTLIER) cc_final: 0.9137 (mm) REVERT: F 37 MET cc_start: 0.9409 (mmm) cc_final: 0.9148 (mmm) REVERT: F 129 MET cc_start: 0.7191 (pmm) cc_final: 0.6471 (pmm) REVERT: F 137 PHE cc_start: 0.9286 (m-10) cc_final: 0.8981 (m-10) REVERT: J 80 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.8125 (t-170) REVERT: J 92 MET cc_start: 0.9610 (mmm) cc_final: 0.8892 (tpt) REVERT: J 108 MET cc_start: 0.9529 (mmp) cc_final: 0.9066 (mmp) REVERT: L 55 MET cc_start: 0.9290 (tpt) cc_final: 0.8662 (tpt) REVERT: N 1 MET cc_start: 0.9057 (pmm) cc_final: 0.8777 (pmm) REVERT: N 20 MET cc_start: 0.9661 (ppp) cc_final: 0.9269 (tmm) REVERT: N 24 MET cc_start: 0.9648 (mmt) cc_final: 0.9325 (mmt) REVERT: N 110 MET cc_start: 0.9012 (mmp) cc_final: 0.8536 (mmm) REVERT: R 40 MET cc_start: 0.8585 (tpt) cc_final: 0.8257 (tpt) REVERT: S 1 MET cc_start: 0.8692 (ppp) cc_final: 0.8440 (ppp) REVERT: S 40 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8163 (p0) REVERT: T 1 MET cc_start: 0.7969 (mtm) cc_final: 0.7578 (mpp) REVERT: V 62 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.8851 (p) REVERT: Z 46 MET cc_start: 0.9595 (mmp) cc_final: 0.9011 (mmm) REVERT: 0 14 MET cc_start: 0.9436 (ttp) cc_final: 0.8630 (ppp) REVERT: K 1 MET cc_start: 0.7950 (tpt) cc_final: 0.7148 (tpp) REVERT: K 7 MET cc_start: 0.9064 (tpt) cc_final: 0.8741 (tpt) REVERT: M 82 MET cc_start: 0.9153 (mmp) cc_final: 0.8322 (mmm) REVERT: M 105 MET cc_start: 0.8508 (mmm) cc_final: 0.8174 (mmm) REVERT: 9 157 MET cc_start: 0.8120 (tpt) cc_final: 0.6951 (tpp) outliers start: 74 outliers final: 40 residues processed: 185 average time/residue: 0.8293 time to fit residues: 277.2967 Evaluate side-chains 162 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 117 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 84 GLU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 53 HIS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 237 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 602 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 356 optimal weight: 30.0000 chunk 456 optimal weight: 30.0000 chunk 353 optimal weight: 20.0000 chunk 526 optimal weight: 30.0000 chunk 349 optimal weight: 30.0000 chunk 622 optimal weight: 6.9990 chunk 389 optimal weight: 30.0000 chunk 379 optimal weight: 30.0000 chunk 287 optimal weight: 8.9990 overall best weight: 13.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 100888 Z= 0.308 Angle : 0.637 13.192 151178 Z= 0.323 Chirality : 0.035 0.367 19351 Planarity : 0.005 0.045 7924 Dihedral : 24.636 177.079 51015 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 37.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.03 % Favored : 91.89 % Rotamer: Outliers : 2.40 % Allowed : 17.65 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.19 (0.14), residues: 3538 helix: -0.03 (0.18), residues: 892 sheet: -0.75 (0.19), residues: 741 loop : -1.14 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 212 HIS 0.013 0.002 HIS O 100 PHE 0.035 0.002 PHE H 29 TYR 0.019 0.002 TYR F 127 ARG 0.009 0.001 ARG O 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 121 time to evaluate : 4.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8233 (p) REVERT: F 37 MET cc_start: 0.9254 (mmm) cc_final: 0.8951 (mmm) REVERT: F 129 MET cc_start: 0.7044 (pmm) cc_final: 0.6364 (pmm) REVERT: F 137 PHE cc_start: 0.9294 (m-10) cc_final: 0.8978 (m-10) REVERT: F 172 PHE cc_start: 0.9283 (m-10) cc_final: 0.9007 (m-80) REVERT: G 148 ARG cc_start: 0.9717 (OUTLIER) cc_final: 0.9511 (ptm160) REVERT: J 80 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.7965 (t-170) REVERT: J 92 MET cc_start: 0.9559 (mmm) cc_final: 0.8975 (tpt) REVERT: J 108 MET cc_start: 0.9529 (mmp) cc_final: 0.9223 (mmp) REVERT: J 118 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8458 (tpp) REVERT: L 55 MET cc_start: 0.9307 (tpt) cc_final: 0.8664 (tpt) REVERT: N 1 MET cc_start: 0.9030 (pmm) cc_final: 0.8751 (pmm) REVERT: N 20 MET cc_start: 0.9666 (ppp) cc_final: 0.9256 (ppp) REVERT: N 24 MET cc_start: 0.9633 (mmt) cc_final: 0.9385 (mmt) REVERT: N 110 MET cc_start: 0.8913 (mmp) cc_final: 0.8510 (mmm) REVERT: R 40 MET cc_start: 0.8831 (tpt) cc_final: 0.8539 (tpt) REVERT: R 49 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6885 (pt) REVERT: S 1 MET cc_start: 0.8701 (ppp) cc_final: 0.8402 (ppp) REVERT: S 40 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8129 (p0) REVERT: V 62 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.8854 (p) REVERT: Y 14 LEU cc_start: 0.9836 (OUTLIER) cc_final: 0.9595 (mt) REVERT: Z 46 MET cc_start: 0.9601 (mmp) cc_final: 0.9009 (mmm) REVERT: K 1 MET cc_start: 0.8180 (tpt) cc_final: 0.7241 (tpp) REVERT: K 7 MET cc_start: 0.8993 (tpt) cc_final: 0.8712 (tpt) REVERT: M 82 MET cc_start: 0.9148 (mmp) cc_final: 0.8326 (mmm) REVERT: M 105 MET cc_start: 0.8502 (mmm) cc_final: 0.8290 (mmm) REVERT: d 1 MET cc_start: 0.8004 (tpp) cc_final: 0.7637 (tpp) REVERT: 9 157 MET cc_start: 0.8154 (tpt) cc_final: 0.6955 (tpp) REVERT: 3 48 MET cc_start: 0.8731 (tpp) cc_final: 0.8439 (tpp) outliers start: 70 outliers final: 49 residues processed: 182 average time/residue: 0.9046 time to fit residues: 298.2086 Evaluate side-chains 176 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 119 time to evaluate : 4.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 84 GLU Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 53 HIS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 200 VAL Chi-restraints excluded: chain 9 residue 237 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 385 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 371 optimal weight: 30.0000 chunk 187 optimal weight: 8.9990 chunk 122 optimal weight: 40.0000 chunk 120 optimal weight: 40.0000 chunk 395 optimal weight: 40.0000 chunk 424 optimal weight: 30.0000 chunk 307 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 489 optimal weight: 30.0000 overall best weight: 16.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 100888 Z= 0.351 Angle : 0.684 13.520 151178 Z= 0.345 Chirality : 0.037 0.361 19351 Planarity : 0.005 0.047 7924 Dihedral : 24.791 177.162 51015 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 41.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.17 % Favored : 91.75 % Rotamer: Outliers : 2.57 % Allowed : 17.89 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.39 (0.14), residues: 3538 helix: -0.20 (0.18), residues: 885 sheet: -0.93 (0.18), residues: 748 loop : -1.24 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 212 HIS 0.019 0.002 HIS V 44 PHE 0.035 0.002 PHE H 29 TYR 0.035 0.002 TYR d 9 ARG 0.009 0.001 ARG Y 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 123 time to evaluate : 4.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8234 (p) REVERT: D 84 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8103 (mp) REVERT: F 37 MET cc_start: 0.9242 (mmm) cc_final: 0.8939 (mmm) REVERT: F 129 MET cc_start: 0.6915 (pmm) cc_final: 0.6313 (pmm) REVERT: F 137 PHE cc_start: 0.9404 (m-10) cc_final: 0.9122 (m-10) REVERT: G 74 MET cc_start: 0.9545 (OUTLIER) cc_final: 0.9334 (ptp) REVERT: J 80 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7876 (t-170) REVERT: J 92 MET cc_start: 0.9602 (mmm) cc_final: 0.8715 (tpp) REVERT: J 108 MET cc_start: 0.9507 (mmp) cc_final: 0.9157 (mmp) REVERT: J 118 MET cc_start: 0.8985 (tpp) cc_final: 0.8581 (tpp) REVERT: L 55 MET cc_start: 0.9324 (tpt) cc_final: 0.8705 (tpt) REVERT: N 1 MET cc_start: 0.9061 (pmm) cc_final: 0.8782 (pmm) REVERT: N 20 MET cc_start: 0.9684 (ppp) cc_final: 0.9263 (ppp) REVERT: N 24 MET cc_start: 0.9627 (mmt) cc_final: 0.9372 (mmt) REVERT: N 110 MET cc_start: 0.8978 (mmp) cc_final: 0.8568 (mmm) REVERT: O 88 LYS cc_start: 0.9286 (mmmt) cc_final: 0.9048 (mmtt) REVERT: Q 51 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8615 (mt0) REVERT: R 40 MET cc_start: 0.8677 (tpt) cc_final: 0.8336 (tpp) REVERT: R 49 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6808 (pt) REVERT: S 1 MET cc_start: 0.8871 (ppp) cc_final: 0.8563 (ppp) REVERT: S 40 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8008 (p0) REVERT: S 82 MET cc_start: 0.9391 (pmm) cc_final: 0.9079 (pmm) REVERT: V 62 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.9012 (p) REVERT: Y 14 LEU cc_start: 0.9830 (OUTLIER) cc_final: 0.9595 (mt) REVERT: Z 46 MET cc_start: 0.9591 (mmp) cc_final: 0.8992 (mmm) REVERT: 0 14 MET cc_start: 0.9325 (ttp) cc_final: 0.8633 (ppp) REVERT: K 1 MET cc_start: 0.8533 (tpt) cc_final: 0.7919 (tpp) REVERT: K 5 GLN cc_start: 0.9585 (OUTLIER) cc_final: 0.8998 (tm-30) REVERT: K 7 MET cc_start: 0.8844 (tpt) cc_final: 0.8565 (tpt) REVERT: K 113 MET cc_start: 0.9278 (mpp) cc_final: 0.8976 (mmm) REVERT: M 82 MET cc_start: 0.9147 (mmp) cc_final: 0.8344 (mmm) REVERT: M 105 MET cc_start: 0.8513 (mmm) cc_final: 0.8289 (mmm) REVERT: d 1 MET cc_start: 0.7980 (tpp) cc_final: 0.7575 (tpp) REVERT: 9 157 MET cc_start: 0.7803 (tpt) cc_final: 0.6819 (tpp) REVERT: 9 271 GLN cc_start: 0.9437 (OUTLIER) cc_final: 0.9102 (pm20) REVERT: 9 289 ASP cc_start: 0.9359 (p0) cc_final: 0.9053 (m-30) outliers start: 75 outliers final: 53 residues processed: 187 average time/residue: 0.8282 time to fit residues: 277.9884 Evaluate side-chains 182 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 118 time to evaluate : 5.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 84 GLU Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 53 HIS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 200 VAL Chi-restraints excluded: chain 9 residue 237 ARG Chi-restraints excluded: chain 9 residue 271 GLN Chi-restraints excluded: chain 9 residue 335 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 566 optimal weight: 30.0000 chunk 596 optimal weight: 30.0000 chunk 544 optimal weight: 30.0000 chunk 580 optimal weight: 30.0000 chunk 349 optimal weight: 30.0000 chunk 252 optimal weight: 10.0000 chunk 455 optimal weight: 30.0000 chunk 178 optimal weight: 30.0000 chunk 524 optimal weight: 70.0000 chunk 548 optimal weight: 30.0000 chunk 578 optimal weight: 30.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN N 11 ASN N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN d 20 ASN 9 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.7840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 100888 Z= 0.543 Angle : 0.879 12.454 151178 Z= 0.436 Chirality : 0.044 0.355 19351 Planarity : 0.006 0.093 7924 Dihedral : 25.179 179.257 51015 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 59.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.12 % Favored : 89.77 % Rotamer: Outliers : 2.91 % Allowed : 18.06 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.95 (0.13), residues: 3538 helix: -0.73 (0.17), residues: 867 sheet: -1.30 (0.18), residues: 743 loop : -1.53 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP J 15 HIS 0.012 0.003 HIS O 34 PHE 0.044 0.003 PHE R 53 TYR 0.026 0.003 TYR G 57 ARG 0.031 0.001 ARG 9 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 117 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8264 (p) REVERT: C 180 MET cc_start: 0.8875 (mmm) cc_final: 0.8213 (mmm) REVERT: D 84 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8479 (mp) REVERT: F 37 MET cc_start: 0.9247 (mmm) cc_final: 0.8947 (mmm) REVERT: F 129 MET cc_start: 0.6390 (pmm) cc_final: 0.5763 (pmm) REVERT: F 137 PHE cc_start: 0.9431 (m-10) cc_final: 0.9152 (m-10) REVERT: G 74 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.9238 (ptp) REVERT: J 80 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.6724 (t-90) REVERT: J 92 MET cc_start: 0.9604 (mmm) cc_final: 0.8727 (tpp) REVERT: J 108 MET cc_start: 0.9521 (mmp) cc_final: 0.9109 (mmp) REVERT: J 118 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8435 (tpp) REVERT: L 55 MET cc_start: 0.9385 (tpt) cc_final: 0.9063 (tpp) REVERT: N 1 MET cc_start: 0.9008 (pmm) cc_final: 0.8747 (pmm) REVERT: N 20 MET cc_start: 0.9691 (ppp) cc_final: 0.9290 (ppp) REVERT: N 24 MET cc_start: 0.9650 (mmt) cc_final: 0.9436 (mmt) REVERT: N 110 MET cc_start: 0.8981 (mmp) cc_final: 0.8553 (mmm) REVERT: Q 51 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8701 (mt0) REVERT: R 40 MET cc_start: 0.8769 (tpt) cc_final: 0.8454 (tpt) REVERT: R 49 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7128 (pt) REVERT: S 40 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.7935 (p0) REVERT: S 82 MET cc_start: 0.8947 (pmm) cc_final: 0.8129 (pmm) REVERT: V 62 THR cc_start: 0.9592 (OUTLIER) cc_final: 0.9177 (p) REVERT: Z 46 MET cc_start: 0.9640 (mmp) cc_final: 0.9030 (mmm) REVERT: K 1 MET cc_start: 0.8658 (tpt) cc_final: 0.7976 (tpp) REVERT: K 5 GLN cc_start: 0.9615 (OUTLIER) cc_final: 0.9132 (tm-30) REVERT: K 113 MET cc_start: 0.9170 (mpp) cc_final: 0.8875 (mmm) REVERT: M 82 MET cc_start: 0.9076 (mmp) cc_final: 0.8210 (mmm) REVERT: M 105 MET cc_start: 0.8836 (mmm) cc_final: 0.8448 (mmm) REVERT: 9 157 MET cc_start: 0.7930 (tpt) cc_final: 0.6951 (tpp) outliers start: 85 outliers final: 55 residues processed: 190 average time/residue: 0.8195 time to fit residues: 278.8021 Evaluate side-chains 181 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 116 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 19 ASN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 84 GLU Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 53 HIS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 200 VAL Chi-restraints excluded: chain 9 residue 237 ARG Chi-restraints excluded: chain 9 residue 335 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 381 optimal weight: 20.0000 chunk 613 optimal weight: 30.0000 chunk 374 optimal weight: 20.0000 chunk 291 optimal weight: 8.9990 chunk 426 optimal weight: 20.0000 chunk 643 optimal weight: 20.0000 chunk 592 optimal weight: 20.0000 chunk 512 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 chunk 395 optimal weight: 40.0000 chunk 314 optimal weight: 20.0000 overall best weight: 14.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN D 36 GLN F 36 ASN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 ASN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN d 20 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.7598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 100888 Z= 0.323 Angle : 0.691 12.910 151178 Z= 0.349 Chirality : 0.037 0.361 19351 Planarity : 0.005 0.098 7924 Dihedral : 25.045 179.186 51015 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 41.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.34 % Favored : 91.58 % Rotamer: Outliers : 2.19 % Allowed : 18.81 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.68 (0.14), residues: 3538 helix: -0.45 (0.17), residues: 880 sheet: -1.21 (0.19), residues: 719 loop : -1.36 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 212 HIS 0.009 0.002 HIS O 34 PHE 0.036 0.002 PHE H 29 TYR 0.030 0.002 TYR G 163 ARG 0.015 0.001 ARG C 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 124 time to evaluate : 4.015 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: C 50 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 131 MET cc_start: 0.9418 (mpp) cc_final: 0.9074 (pmm) REVERT: C 180 MET cc_start: 0.8759 (mmm) cc_final: 0.8306 (mmm) REVERT: D 84 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8513 (mp) REVERT: F 37 MET cc_start: 0.9211 (mmm) cc_final: 0.8905 (mmm) REVERT: F 129 MET cc_start: 0.6407 (pmm) cc_final: 0.5699 (pmm) REVERT: F 137 PHE cc_start: 0.9441 (m-10) cc_final: 0.9156 (m-10) REVERT: G 74 MET cc_start: 0.9550 (OUTLIER) cc_final: 0.9337 (ptp) REVERT: J 80 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.5726 (t-90) REVERT: J 92 MET cc_start: 0.9544 (mmm) cc_final: 0.8604 (tpp) REVERT: J 108 MET cc_start: 0.9510 (mmp) cc_final: 0.9140 (mmp) REVERT: J 118 MET cc_start: 0.8777 (tpp) cc_final: 0.8375 (tpp) REVERT: L 55 MET cc_start: 0.9307 (tpt) cc_final: 0.8714 (tpt) REVERT: N 1 MET cc_start: 0.9108 (pmm) cc_final: 0.8833 (pmm) REVERT: N 20 MET cc_start: 0.9689 (ppp) cc_final: 0.9342 (tmm) REVERT: N 24 MET cc_start: 0.9640 (mmt) cc_final: 0.9189 (mmt) REVERT: N 110 MET cc_start: 0.8932 (mmp) cc_final: 0.8564 (mmm) REVERT: O 88 LYS cc_start: 0.9296 (mmmt) cc_final: 0.9087 (mmtt) REVERT: Q 51 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: R 40 MET cc_start: 0.8696 (tpt) cc_final: 0.8366 (tpt) REVERT: R 49 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6815 (pt) REVERT: S 1 MET cc_start: 0.8860 (ppp) cc_final: 0.8499 (ppp) REVERT: S 40 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.7963 (p0) REVERT: S 82 MET cc_start: 0.9220 (pmm) cc_final: 0.8947 (pmm) REVERT: V 51 GLN cc_start: 0.9523 (OUTLIER) cc_final: 0.9170 (pp30) REVERT: V 62 THR cc_start: 0.9600 (OUTLIER) cc_final: 0.9211 (p) REVERT: Y 1 MET cc_start: 0.9208 (tmm) cc_final: 0.8975 (tmm) REVERT: Z 46 MET cc_start: 0.9669 (mmp) cc_final: 0.8939 (mmm) REVERT: K 1 MET cc_start: 0.8579 (tpt) cc_final: 0.7911 (tpp) REVERT: K 5 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9116 (tm-30) REVERT: K 7 MET cc_start: 0.8712 (tpp) cc_final: 0.8111 (tpp) REVERT: K 20 MET cc_start: 0.9084 (tpp) cc_final: 0.8721 (tpp) REVERT: K 113 MET cc_start: 0.9153 (mpp) cc_final: 0.8883 (mmm) REVERT: M 82 MET cc_start: 0.9182 (mmp) cc_final: 0.8387 (mmm) REVERT: M 105 MET cc_start: 0.8526 (mmm) cc_final: 0.8250 (mmm) REVERT: 9 108 MET cc_start: 0.8881 (mmp) cc_final: 0.8279 (mmp) REVERT: 9 157 MET cc_start: 0.8285 (tpt) cc_final: 0.7420 (tpp) outliers start: 64 outliers final: 47 residues processed: 178 average time/residue: 0.8174 time to fit residues: 261.7307 Evaluate side-chains 180 residues out of total 2919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 123 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 173 ASP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain V residue 35 GLU Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain W residue 53 HIS Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain K residue 5 GLN Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain d residue 22 MET Chi-restraints excluded: chain 9 residue 12 VAL Chi-restraints excluded: chain 9 residue 174 THR Chi-restraints excluded: chain 9 residue 200 VAL Chi-restraints excluded: chain 9 residue 237 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 646 random chunks: chunk 407 optimal weight: 30.0000 chunk 545 optimal weight: 40.0000 chunk 157 optimal weight: 7.9990 chunk 472 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 513 optimal weight: 30.0000 chunk 214 optimal weight: 0.0470 chunk 527 optimal weight: 40.0000 chunk 64 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 13 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN L 54 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.023237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.018664 restraints weight = 1960632.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.019042 restraints weight = 706380.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.019331 restraints weight = 396988.488| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.6966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 100888 Z= 0.155 Angle : 0.566 17.272 151178 Z= 0.288 Chirality : 0.032 0.362 19351 Planarity : 0.004 0.124 7924 Dihedral : 24.586 178.361 51015 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.90 % Favored : 93.02 % Rotamer: Outliers : 1.23 % Allowed : 19.60 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.13 (0.14), residues: 3538 helix: -0.04 (0.18), residues: 885 sheet: -0.60 (0.19), residues: 702 loop : -1.11 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 212 HIS 0.007 0.001 HIS Z 33 PHE 0.026 0.002 PHE H 29 TYR 0.025 0.001 TYR G 163 ARG 0.015 0.001 ARG F 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9268.63 seconds wall clock time: 174 minutes 57.67 seconds (10497.67 seconds total)