Starting phenix.real_space_refine on Mon Mar 18 06:52:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yan_10762/03_2024/6yan_10762_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yan_10762/03_2024/6yan_10762.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yan_10762/03_2024/6yan_10762_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yan_10762/03_2024/6yan_10762_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yan_10762/03_2024/6yan_10762_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yan_10762/03_2024/6yan_10762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yan_10762/03_2024/6yan_10762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yan_10762/03_2024/6yan_10762_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yan_10762/03_2024/6yan_10762_updated.pdb" } resolution = 3.48 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1849 5.49 5 S 217 5.16 5 C 45893 2.51 5 N 15448 2.21 5 O 20844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "l ARG 9": "NH1" <-> "NH2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G ARG 252": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 160": "OE1" <-> "OE2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I GLU 35": "OE1" <-> "OE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I GLU 118": "OE1" <-> "OE2" Residue "I ARG 131": "NH1" <-> "NH2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I GLU 204": "OE1" <-> "OE2" Residue "J GLU 14": "OE1" <-> "OE2" Residue "J GLU 18": "OE1" <-> "OE2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 81": "NH1" <-> "NH2" Residue "J ARG 99": "NH1" <-> "NH2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 191": "OE1" <-> "OE2" Residue "K ARG 25": "NH1" <-> "NH2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K GLU 114": "OE1" <-> "OE2" Residue "K GLU 151": "OE1" <-> "OE2" Residue "K GLU 163": "OE1" <-> "OE2" Residue "K GLU 191": "OE1" <-> "OE2" Residue "K GLU 194": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "M GLU 13": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M GLU 34": "OE1" <-> "OE2" Residue "M GLU 60": "OE1" <-> "OE2" Residue "M TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "N GLU 49": "OE1" <-> "OE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O GLU 87": "OE1" <-> "OE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P GLU 103": "OE1" <-> "OE2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q GLU 25": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q ARG 150": "NH1" <-> "NH2" Residue "S GLU 40": "OE1" <-> "OE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 102": "OE1" <-> "OE2" Residue "S ARG 126": "NH1" <-> "NH2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S ARG 140": "NH1" <-> "NH2" Residue "S ARG 146": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T GLU 79": "OE1" <-> "OE2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T GLU 97": "OE1" <-> "OE2" Residue "V GLU 13": "OE1" <-> "OE2" Residue "V GLU 32": "OE1" <-> "OE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "V ARG 102": "NH1" <-> "NH2" Residue "V GLU 108": "OE1" <-> "OE2" Residue "V ARG 121": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 87": "NH1" <-> "NH2" Residue "W GLU 107": "OE1" <-> "OE2" Residue "X GLU 7": "OE1" <-> "OE2" Residue "X GLU 38": "OE1" <-> "OE2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "Y GLU 51": "OE1" <-> "OE2" Residue "Y GLU 87": "OE1" <-> "OE2" Residue "Y PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 115": "OE1" <-> "OE2" Residue "Z ARG 5": "NH1" <-> "NH2" Residue "Z ARG 8": "NH1" <-> "NH2" Residue "Z ARG 17": "NH1" <-> "NH2" Residue "Z GLU 53": "OE1" <-> "OE2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z GLU 96": "OE1" <-> "OE2" Residue "Z GLU 99": "OE1" <-> "OE2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "a ARG 20": "NH1" <-> "NH2" Residue "a GLU 39": "OE1" <-> "OE2" Residue "a GLU 42": "OE1" <-> "OE2" Residue "a ARG 61": "NH1" <-> "NH2" Residue "a GLU 109": "OE1" <-> "OE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b GLU 46": "OE1" <-> "OE2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "c GLU 13": "OE1" <-> "OE2" Residue "c GLU 15": "OE1" <-> "OE2" Residue "c GLU 75": "OE1" <-> "OE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 33": "OE1" <-> "OE2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d GLU 60": "OE1" <-> "OE2" Residue "d GLU 62": "OE1" <-> "OE2" Residue "d ARG 63": "NH1" <-> "NH2" Residue "e ARG 27": "NH1" <-> "NH2" Residue "f GLU 125": "OE1" <-> "OE2" Residue "g GLU 3": "OE1" <-> "OE2" Residue "g GLU 49": "OE1" <-> "OE2" Residue "g GLU 149": "OE1" <-> "OE2" Residue "g GLU 223": "OE1" <-> "OE2" Residue "g GLU 273": "OE1" <-> "OE2" Residue "g GLU 282": "OE1" <-> "OE2" Residue "h GLU 75": "OE1" <-> "OE2" Residue "h ARG 80": "NH1" <-> "NH2" Residue "i ARG 105": "NH1" <-> "NH2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "U ARG 39": "NH1" <-> "NH2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 142": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 84251 Number of models: 1 Model: "" Number of chains: 39 Chain: "l" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 240 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1643 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1742 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 209} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1743 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 212} Chain: "G" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2083 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain: "H" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1509 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "I" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1924 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain breaks: 1 Chain: "J" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1530 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 180} Chain: "K" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1680 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 197} Chain: "L" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "M" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 828 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 89} Chain: "N" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1296 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 149} Chain: "O" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "S" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1123 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "T" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1020 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 118} Chain: "V" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1113 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "W" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "X" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 78} Chain: "Y" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1107 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 136} Chain: "a" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1022 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain breaks: 1 Chain: "b" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "c" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 76} Chain: "d" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 445 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "f" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 582 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 67} Chain: "g" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2437 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 300} Chain: "h" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 599 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "i" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 473 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 55} Chain: "2" Number of atoms: 37202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1744, 37202 Inner-chain residues flagged as termini: ['pdbres=" C 2 139 "', 'pdbres=" G 2 270 "', 'pdbres=" G 21765 "'] Classifications: {'RNA': 1744} Modifications used: {'5*END': 4, 'rna2p_pur': 146, 'rna2p_pyr': 118, 'rna3p': 1, 'rna3p_pur': 766, 'rna3p_pyr': 711} Link IDs: {'rna2p': 264, 'rna3p': 1479} Unresolved chain links: 1 Chain breaks: 3 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 774 Classifications: {'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 20, 'rna3p_pyr': 10} Link IDs: {'rna2p': 6, 'rna3p': 29} Chain: "A" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2147 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain: "B" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3214 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'CIS': 7, 'PTRANS': 22, 'TRANS': 392} Chain: "U" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1172 Classifications: {'peptide': 142} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 138} Chain: "R" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 126} Chain: "1" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1614 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 11, 'rna3p': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 33.08, per 1000 atoms: 0.39 Number of scatterers: 84251 At special positions: 0 Unit cell: (229.9, 236.5, 203.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 217 16.00 P 1849 15.00 O 20844 8.00 N 15448 7.00 C 45893 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=2.03 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 Atom "ATOM 51061 O4' G 2 740 .*. O " rejected from bonding due to valence issues. Atom "ATOM 51021 O4' U 2 738 .*. O " rejected from bonding due to valence issues. Atom "ATOM 51021 O4' U 2 738 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.69 Conformation dependent library (CDL) restraints added in 6.7 seconds 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 153 helices and 63 sheets defined 27.0% alpha, 14.8% beta 506 base pairs and 863 stacking pairs defined. Time for finding SS restraints: 32.41 Creating SS restraints... Processing helix chain 'l' and resid 2 through 24 removed outlier: 3.545A pdb=" N MET l 10 " --> pdb=" O ARG l 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 4.039A pdb=" N LEU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.814A pdb=" N LYS C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 removed outlier: 4.271A pdb=" N ARG C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA C 86 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 87 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.964A pdb=" N SER C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR C 139 " --> pdb=" O THR C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 186 removed outlier: 4.042A pdb=" N VAL C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 172 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU C 173 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 177 " --> pdb=" O MET C 174 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 178 " --> pdb=" O TRP C 175 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 182 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 183 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 185 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG C 186 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 72 through 75 No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 158 through 177 removed outlier: 3.731A pdb=" N ILE D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET D 172 " --> pdb=" O MET D 168 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 189 Processing helix chain 'D' and resid 192 through 200 removed outlier: 3.711A pdb=" N LYS D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.764A pdb=" N LEU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 57 removed outlier: 3.528A pdb=" N VAL E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 removed outlier: 3.720A pdb=" N PHE E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 82 No H-bonds generated for 'chain 'E' and resid 79 through 82' Processing helix chain 'E' and resid 132 through 146 removed outlier: 3.603A pdb=" N SER E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 202 removed outlier: 3.950A pdb=" N LEU E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 234 removed outlier: 3.551A pdb=" N LYS E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 Processing helix chain 'E' and resid 250 through 253 No H-bonds generated for 'chain 'E' and resid 250 through 253' Processing helix chain 'E' and resid 255 through 258 No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.878A pdb=" N PHE F 11 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN F 22 " --> pdb=" O LYS F 18 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 64 through 76 removed outlier: 3.623A pdb=" N LYS F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.512A pdb=" N TYR F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 128 removed outlier: 3.645A pdb=" N PHE F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 4.025A pdb=" N TYR F 167 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 40 No H-bonds generated for 'chain 'G' and resid 38 through 40' Processing helix chain 'G' and resid 44 through 49 removed outlier: 4.294A pdb=" N ARG G 49 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 67 removed outlier: 4.061A pdb=" N GLN G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 248 through 258 removed outlier: 3.760A pdb=" N ARG G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 74 Processing helix chain 'H' and resid 86 through 104 removed outlier: 3.587A pdb=" N ARG H 91 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE H 92 " --> pdb=" O MET H 88 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS H 95 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 117 removed outlier: 3.549A pdb=" N LEU H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 163 removed outlier: 3.734A pdb=" N LEU H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS H 155 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA H 158 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE H 163 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 removed outlier: 3.554A pdb=" N ILE H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 202 removed outlier: 3.655A pdb=" N LYS H 192 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP H 194 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER H 202 " --> pdb=" O ARG H 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 24 No H-bonds generated for 'chain 'I' and resid 21 through 24' Processing helix chain 'I' and resid 138 through 145 Processing helix chain 'I' and resid 182 through 235 removed outlier: 3.541A pdb=" N HIS I 187 " --> pdb=" O ARG I 183 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS I 195 " --> pdb=" O ARG I 191 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA I 206 " --> pdb=" O ASN I 202 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS I 218 " --> pdb=" O ALA I 214 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU I 219 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS I 221 " --> pdb=" O MET I 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 32 removed outlier: 3.699A pdb=" N ALA J 26 " --> pdb=" O GLY J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 75 removed outlier: 3.642A pdb=" N GLN J 73 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE J 75 " --> pdb=" O PHE J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 86 Processing helix chain 'J' and resid 123 through 133 removed outlier: 3.742A pdb=" N LEU J 130 " --> pdb=" O HIS J 126 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU J 131 " --> pdb=" O ASP J 127 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP J 132 " --> pdb=" O ALA J 128 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU J 133 " --> pdb=" O ILE J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 172 through 180 removed outlier: 3.646A pdb=" N LYS J 179 " --> pdb=" O GLY J 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 92 No H-bonds generated for 'chain 'K' and resid 89 through 92' Processing helix chain 'K' and resid 107 through 116 removed outlier: 3.601A pdb=" N GLN K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 152 removed outlier: 5.292A pdb=" N GLU K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG K 152 " --> pdb=" O LYS K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 168 removed outlier: 4.252A pdb=" N GLN K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN K 167 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN K 168 " --> pdb=" O GLU K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 182 No H-bonds generated for 'chain 'K' and resid 179 through 182' Processing helix chain 'K' and resid 192 through 205 Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.572A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 60 removed outlier: 3.984A pdb=" N TRP L 44 " --> pdb=" O ARG L 41 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG L 45 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU L 50 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG L 54 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA L 56 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA L 57 " --> pdb=" O ARG L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 84 removed outlier: 3.527A pdb=" N ARG L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 102 through 108 removed outlier: 3.577A pdb=" N LEU L 106 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG L 108 " --> pdb=" O ASP L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 117 Processing helix chain 'L' and resid 123 through 131 removed outlier: 4.049A pdb=" N VAL L 128 " --> pdb=" O HIS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 153 No H-bonds generated for 'chain 'L' and resid 151 through 153' Processing helix chain 'L' and resid 174 through 178 Processing helix chain 'M' and resid 6 through 18 removed outlier: 3.686A pdb=" N ILE M 11 " --> pdb=" O ASN M 7 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 55 removed outlier: 3.990A pdb=" N SER M 51 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 82 Processing helix chain 'N' and resid 48 through 52 Processing helix chain 'O' and resid 14 through 28 removed outlier: 4.106A pdb=" N THR O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 43 Processing helix chain 'O' and resid 61 through 71 removed outlier: 3.831A pdb=" N GLU O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 120 through 129 removed outlier: 3.916A pdb=" N ILE O 124 " --> pdb=" O LYS O 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU O 125 " --> pdb=" O ASP O 122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU O 126 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR O 127 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS O 129 " --> pdb=" O GLU O 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 43 removed outlier: 3.578A pdb=" N LYS P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU P 40 " --> pdb=" O GLN P 36 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS P 42 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 55 Processing helix chain 'P' and resid 71 through 78 removed outlier: 3.769A pdb=" N LYS P 78 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 104 removed outlier: 3.774A pdb=" N VAL P 96 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA P 97 " --> pdb=" O LYS P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 132 removed outlier: 3.715A pdb=" N ILE P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU P 117 " --> pdb=" O PHE P 113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS P 123 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR P 131 " --> pdb=" O ARG P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 150 Processing helix chain 'Q' and resid 58 through 61 No H-bonds generated for 'chain 'Q' and resid 58 through 61' Processing helix chain 'Q' and resid 71 through 88 removed outlier: 4.546A pdb=" N GLN Q 83 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 123 removed outlier: 3.605A pdb=" N GLY Q 123 " --> pdb=" O LEU Q 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 51 No H-bonds generated for 'chain 'S' and resid 48 through 51' Processing helix chain 'S' and resid 53 through 58 Processing helix chain 'S' and resid 77 through 99 removed outlier: 3.821A pdb=" N ILE S 81 " --> pdb=" O HIS S 77 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL S 93 " --> pdb=" O SER S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 114 removed outlier: 3.823A pdb=" N GLU S 107 " --> pdb=" O ALA S 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE S 108 " --> pdb=" O SER S 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 18 removed outlier: 3.617A pdb=" N ALA T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG T 14 " --> pdb=" O LYS T 10 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL T 15 " --> pdb=" O LYS T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 21 through 23 No H-bonds generated for 'chain 'T' and resid 21 through 23' Processing helix chain 'T' and resid 28 through 38 Processing helix chain 'T' and resid 45 through 63 removed outlier: 3.859A pdb=" N GLY T 52 " --> pdb=" O ASN T 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG T 60 " --> pdb=" O HIS T 56 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN T 62 " --> pdb=" O MET T 58 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG T 63 " --> pdb=" O LYS T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 82 Processing helix chain 'T' and resid 103 through 107 Processing helix chain 'V' and resid 6 through 8 No H-bonds generated for 'chain 'V' and resid 6 through 8' Processing helix chain 'V' and resid 11 through 24 removed outlier: 4.055A pdb=" N ARG V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA V 20 " --> pdb=" O ARG V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 66 removed outlier: 3.501A pdb=" N SER V 59 " --> pdb=" O THR V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 72 through 79 Processing helix chain 'V' and resid 98 through 109 Processing helix chain 'V' and resid 125 through 141 removed outlier: 3.535A pdb=" N ASP V 132 " --> pdb=" O GLN V 128 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY V 136 " --> pdb=" O ASP V 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN V 137 " --> pdb=" O ARG V 133 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA V 139 " --> pdb=" O ALA V 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 44 removed outlier: 3.779A pdb=" N VAL W 35 " --> pdb=" O SER W 31 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA W 43 " --> pdb=" O LEU W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 102 Processing helix chain 'X' and resid 57 through 62 Processing helix chain 'X' and resid 65 through 74 removed outlier: 3.537A pdb=" N LEU X 70 " --> pdb=" O ASP X 66 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 20 removed outlier: 3.510A pdb=" N LEU Y 11 " --> pdb=" O LEU Y 7 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS Y 12 " --> pdb=" O ALA Y 8 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER Y 13 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG Y 20 " --> pdb=" O ASN Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 44 removed outlier: 3.640A pdb=" N HIS Y 44 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 93 removed outlier: 3.660A pdb=" N ASN Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 119 removed outlier: 3.998A pdb=" N ARG Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 14 Processing helix chain 'Z' and resid 17 through 20 No H-bonds generated for 'chain 'Z' and resid 17 through 20' Processing helix chain 'Z' and resid 25 through 30 removed outlier: 3.560A pdb=" N LYS Z 29 " --> pdb=" O LYS Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 38 Processing helix chain 'Z' and resid 130 through 135 Processing helix chain 'a' and resid 37 through 48 removed outlier: 3.550A pdb=" N LYS a 43 " --> pdb=" O GLU a 39 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET a 47 " --> pdb=" O LYS a 43 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR a 48 " --> pdb=" O LEU a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 85 Processing helix chain 'a' and resid 88 through 91 No H-bonds generated for 'chain 'a' and resid 88 through 91' Processing helix chain 'a' and resid 106 through 114 removed outlier: 3.592A pdb=" N ARG a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 126 No H-bonds generated for 'chain 'a' and resid 123 through 126' Processing helix chain 'b' and resid 50 through 54 Processing helix chain 'b' and resid 75 through 81 removed outlier: 3.651A pdb=" N ILE b 79 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER b 81 " --> pdb=" O CYS b 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 18 No H-bonds generated for 'chain 'e' and resid 16 through 18' Processing helix chain 'e' and resid 33 through 35 No H-bonds generated for 'chain 'e' and resid 33 through 35' Processing helix chain 'e' and resid 40 through 43 No H-bonds generated for 'chain 'e' and resid 40 through 43' Processing helix chain 'h' and resid 52 through 60 removed outlier: 3.617A pdb=" N LYS h 60 " --> pdb=" O ASP h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 76 removed outlier: 3.663A pdb=" N GLU h 75 " --> pdb=" O ALA h 71 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 94 removed outlier: 3.610A pdb=" N LEU h 91 " --> pdb=" O ALA h 87 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS h 94 " --> pdb=" O GLU h 90 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 115 removed outlier: 3.940A pdb=" N ARG i 108 " --> pdb=" O GLY i 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN i 111 " --> pdb=" O LYS i 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 114 removed outlier: 3.968A pdb=" N HIS A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 139 removed outlier: 3.944A pdb=" N LEU A 127 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 133 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 134 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA A 135 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TRP A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 137 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.760A pdb=" N SER A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.799A pdb=" N LYS A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 3.649A pdb=" N MET A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'B' and resid 68 through 74 Processing helix chain 'B' and resid 152 through 164 removed outlier: 4.590A pdb=" N ALA B 156 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 159 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.491A pdb=" N GLN B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 254 removed outlier: 3.580A pdb=" N GLU B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 253 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 361 Processing helix chain 'U' and resid 26 through 32 removed outlier: 3.506A pdb=" N THR U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA U 32 " --> pdb=" O PHE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 39 through 47 removed outlier: 3.994A pdb=" N VAL U 43 " --> pdb=" O ARG U 39 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL U 44 " --> pdb=" O TYR U 40 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG U 46 " --> pdb=" O HIS U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 58 No H-bonds generated for 'chain 'U' and resid 56 through 58' Processing helix chain 'U' and resid 61 through 72 removed outlier: 3.647A pdb=" N ARG U 66 " --> pdb=" O ASP U 62 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE U 68 " --> pdb=" O VAL U 64 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR U 69 " --> pdb=" O GLU U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'U' and resid 81 through 83 No H-bonds generated for 'chain 'U' and resid 81 through 83' Processing helix chain 'U' and resid 100 through 116 removed outlier: 3.866A pdb=" N ASP U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN U 105 " --> pdb=" O ASN U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 127 Processing helix chain 'R' and resid 17 through 19 No H-bonds generated for 'chain 'R' and resid 17 through 19' Processing helix chain 'R' and resid 22 through 25 No H-bonds generated for 'chain 'R' and resid 22 through 25' Processing helix chain 'R' and resid 30 through 34 Processing helix chain 'R' and resid 39 through 46 removed outlier: 3.664A pdb=" N LEU R 45 " --> pdb=" O ARG R 42 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER R 46 " --> pdb=" O ARG R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 66 removed outlier: 3.971A pdb=" N ARG R 59 " --> pdb=" O SER R 55 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 118 No H-bonds generated for 'chain 'R' and resid 116 through 118' Processing sheet with id= A, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.865A pdb=" N THR C 97 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 121 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE C 77 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 123 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 145 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 38 through 41 removed outlier: 7.152A pdb=" N ILE C 48 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 28 through 30 Processing sheet with id= D, first strand: chain 'D' and resid 120 through 128 removed outlier: 4.037A pdb=" N ALA D 123 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS D 214 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL D 140 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL D 212 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHE D 142 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D 210 " --> pdb=" O PHE D 142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 84 through 88 removed outlier: 4.103A pdb=" N GLY D 102 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE D 87 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N PHE D 100 " --> pdb=" O ILE D 87 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 122 through 129 removed outlier: 3.881A pdb=" N LYS E 93 " --> pdb=" O PHE E 112 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA E 114 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL E 91 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLY E 116 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP E 89 " --> pdb=" O GLY E 116 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.803A pdb=" N GLU F 89 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 148 through 155 removed outlier: 4.186A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 70 through 72 removed outlier: 3.500A pdb=" N SER G 91 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE G 90 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 121 through 125 removed outlier: 3.735A pdb=" N THR G 159 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP G 171 " --> pdb=" O GLN G 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 146 through 148 removed outlier: 3.866A pdb=" N ILE G 147 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS G 128 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 192 through 194 removed outlier: 3.531A pdb=" N GLY G 229 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N MET G 182 " --> pdb=" O VAL G 227 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL G 227 " --> pdb=" O MET G 182 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 207 through 211 Processing sheet with id= N, first strand: chain 'H' and resid 124 through 130 removed outlier: 3.616A pdb=" N ARG H 135 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG H 130 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 12 through 17 removed outlier: 3.571A pdb=" N ILE I 16 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU I 109 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL I 49 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 72 through 77 removed outlier: 3.541A pdb=" N LYS I 95 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS I 93 " --> pdb=" O LEU I 77 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 54 through 57 removed outlier: 4.086A pdb=" N GLY I 54 " --> pdb=" O ASN I 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL I 108 " --> pdb=" O ASN I 56 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 47 through 52 removed outlier: 4.315A pdb=" N ALA J 47 " --> pdb=" O PHE J 63 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N HIS J 91 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE J 62 " --> pdb=" O HIS J 91 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL J 93 " --> pdb=" O ILE J 62 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 139 through 146 removed outlier: 6.898A pdb=" N HIS J 157 " --> pdb=" O VAL J 140 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS J 142 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS J 155 " --> pdb=" O LYS J 142 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE J 144 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU J 153 " --> pdb=" O ILE J 144 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 62 through 67 removed outlier: 3.657A pdb=" N PHE K 65 " --> pdb=" O ARG K 74 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 187 through 189 removed outlier: 4.638A pdb=" N CYS K 100 " --> pdb=" O ILE K 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR K 83 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU K 103 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL K 81 " --> pdb=" O LEU K 103 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 42 through 48 removed outlier: 4.955A pdb=" N ASN K 52 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 135 through 137 removed outlier: 3.577A pdb=" N ASP L 158 " --> pdb=" O ARG L 136 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 20 through 24 removed outlier: 3.783A pdb=" N ALA M 23 " --> pdb=" O PHE M 67 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 102 through 112 removed outlier: 4.002A pdb=" N LYS N 79 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG N 89 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL N 77 " --> pdb=" O ARG N 89 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASP N 91 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N GLY N 75 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 15.610A pdb=" N LEU N 93 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 16.553A pdb=" N LEU N 73 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL N 126 " --> pdb=" O GLY N 75 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS N 144 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY N 129 " --> pdb=" O VAL N 142 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL N 142 " --> pdb=" O GLY N 129 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 49 through 52 Processing sheet with id= AA, first strand: chain 'Q' and resid 28 through 30 removed outlier: 6.795A pdb=" N ALA Q 92 " --> pdb=" O GLY Q 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'Q' and resid 41 through 43 Processing sheet with id= AC, first strand: chain 'S' and resid 9 through 12 Processing sheet with id= AD, first strand: chain 'V' and resid 113 through 116 removed outlier: 3.582A pdb=" N GLY V 120 " --> pdb=" O ASP V 116 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'W' and resid 85 through 94 removed outlier: 3.684A pdb=" N THR W 25 " --> pdb=" O GLU W 111 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'W' and resid 59 through 66 removed outlier: 3.733A pdb=" N LYS W 59 " --> pdb=" O ILE W 84 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR W 65 " --> pdb=" O ASP W 78 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'X' and resid 32 through 37 Processing sheet with id= AH, first strand: chain 'Y' and resid 50 through 53 Processing sheet with id= AI, first strand: chain 'Y' and resid 71 through 74 removed outlier: 3.809A pdb=" N LYS Y 71 " --> pdb=" O PHE Y 130 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU Y 126 " --> pdb=" O VAL Y 103 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL Y 103 " --> pdb=" O LEU Y 126 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE Y 128 " --> pdb=" O PHE Y 101 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE Y 101 " --> pdb=" O PHE Y 128 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Z' and resid 80 through 83 removed outlier: 3.524A pdb=" N GLU Z 53 " --> pdb=" O ARG Z 71 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN Z 73 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL Z 51 " --> pdb=" O GLN Z 73 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA Z 47 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS Z 124 " --> pdb=" O LEU Z 101 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA Z 103 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL Z 122 " --> pdb=" O ALA Z 103 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'a' and resid 6 through 8 removed outlier: 3.752A pdb=" N ASP a 26 " --> pdb=" O ARG a 8 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'a' and resid 13 through 15 Processing sheet with id= AM, first strand: chain 'b' and resid 20 through 22 Processing sheet with id= AN, first strand: chain 'b' and resid 36 through 43 removed outlier: 3.848A pdb=" N VAL b 69 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'c' and resid 32 through 35 Processing sheet with id= AP, first strand: chain 'd' and resid 55 through 58 removed outlier: 3.709A pdb=" N ALA d 12 " --> pdb=" O LEU d 56 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'd' and resid 19 through 21 removed outlier: 3.648A pdb=" N GLY d 19 " --> pdb=" O GLN d 29 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'f' and resid 106 through 108 Processing sheet with id= AS, first strand: chain 'g' and resid 99 through 101 removed outlier: 3.503A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG g 88 " --> pdb=" O SER g 80 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA g 78 " --> pdb=" O TRP g 90 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'g' and resid 108 through 113 removed outlier: 6.585A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER g 122 " --> pdb=" O LYS g 130 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS g 130 " --> pdb=" O SER g 122 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR g 140 " --> pdb=" O LEU g 131 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'g' and resid 151 through 156 removed outlier: 6.870A pdb=" N CYS g 168 " --> pdb=" O SER g 152 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL g 154 " --> pdb=" O VAL g 166 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL g 166 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR g 186 " --> pdb=" O VAL g 176 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 218 through 220 removed outlier: 3.756A pdb=" N THR g 197 " --> pdb=" O GLY g 210 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 215 through 217 Processing sheet with id= AX, first strand: chain 'g' and resid 239 through 241 removed outlier: 3.650A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 4 through 12 removed outlier: 6.828A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU g 306 " --> pdb=" O TYR g 302 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER g 288 " --> pdb=" O GLY g 301 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 40 through 45 removed outlier: 3.676A pdb=" N ILE g 40 " --> pdb=" O LEU g 59 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'h' and resid 98 through 102 removed outlier: 3.574A pdb=" N VAL h 100 " --> pdb=" O ILE h 108 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE h 108 " --> pdb=" O VAL h 100 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'A' and resid 43 through 47 removed outlier: 7.158A pdb=" N ASP A 84 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 76 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 82 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'A' and resid 226 through 231 removed outlier: 4.190A pdb=" N ILE A 230 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ARG A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'B' and resid 234 through 236 removed outlier: 6.294A pdb=" N ILE B 200 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 199 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 170 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 60 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ILE B 57 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER B 144 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR B 59 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 146 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE B 101 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N HIS B 142 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 99 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER B 144 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'B' and resid 369 through 372 removed outlier: 3.993A pdb=" N LYS B 298 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 270 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE B 296 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'B' and resid 273 through 275 Processing sheet with id= BG, first strand: chain 'B' and resid 306 through 309 Processing sheet with id= BH, first strand: chain 'B' and resid 379 through 381 Processing sheet with id= BI, first strand: chain 'B' and resid 438 through 441 removed outlier: 3.971A pdb=" N GLU B 385 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 456 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP B 469 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE B 454 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER B 457 " --> pdb=" O MET B 418 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N MET B 418 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ARG B 459 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N VAL B 416 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS B 439 " --> pdb=" O SER B 431 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL B 433 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'U' and resid 13 through 15 removed outlier: 3.653A pdb=" N VAL U 15 " --> pdb=" O THR U 18 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR U 18 " --> pdb=" O VAL U 15 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'R' and resid 76 through 78 1152 hydrogen bonds defined for protein. 3147 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1263 hydrogen bonds 2030 hydrogen bond angles 0 basepair planarities 506 basepair parallelities 863 stacking parallelities Total time for adding SS restraints: 60.03 Time building geometry restraints manager: 34.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.28: 9001 1.28 - 1.50: 50053 1.50 - 1.71: 30282 1.71 - 1.92: 334 1.92 - 2.13: 2 Bond restraints: 89672 Sorted by residual: bond pdb=" O3' G 1 19 " pdb=" P A 1 20 " ideal model delta sigma weight residual 1.607 2.129 -0.522 1.50e-02 4.44e+03 1.21e+03 bond pdb=" O3' G 1 16 " pdb=" P C 1 17 " ideal model delta sigma weight residual 1.607 1.137 0.470 1.50e-02 4.44e+03 9.82e+02 bond pdb=" O3' C 1 17 " pdb=" P G 1 18 " ideal model delta sigma weight residual 1.607 1.992 -0.385 1.50e-02 4.44e+03 6.60e+02 bond pdb=" O3' U 21815 " pdb=" P A 21816 " ideal model delta sigma weight residual 1.607 1.256 0.351 1.50e-02 4.44e+03 5.47e+02 bond pdb=" C2' C 1 17 " pdb=" O2' C 1 17 " ideal model delta sigma weight residual 1.412 1.073 0.339 1.50e-02 4.44e+03 5.10e+02 ... (remaining 89667 not shown) Histogram of bond angle deviations from ideal: 67.51 - 86.93: 6 86.93 - 106.35: 13529 106.35 - 125.77: 109774 125.77 - 145.19: 6631 145.19 - 164.60: 4 Bond angle restraints: 129944 Sorted by residual: angle pdb=" O3' G 1 19 " pdb=" P A 1 20 " pdb=" O5' A 1 20 " ideal model delta sigma weight residual 104.00 164.60 -60.60 1.50e+00 4.44e-01 1.63e+03 angle pdb=" C4' C 1 17 " pdb=" C3' C 1 17 " pdb=" O3' C 1 17 " ideal model delta sigma weight residual 109.40 145.59 -36.19 1.50e+00 4.44e-01 5.82e+02 angle pdb=" O3' U 2 797 " pdb=" P A 2 798 " pdb=" O5' A 2 798 " ideal model delta sigma weight residual 104.00 70.15 33.85 1.50e+00 4.44e-01 5.09e+02 angle pdb=" O3' U 2 676 " pdb=" P C 2 677 " pdb=" O5' C 2 677 " ideal model delta sigma weight residual 104.00 70.62 33.38 1.50e+00 4.44e-01 4.95e+02 angle pdb=" C ARG A 54 " pdb=" N ARG A 55 " pdb=" CA ARG A 55 " ideal model delta sigma weight residual 122.30 151.05 -28.75 1.35e+00 5.49e-01 4.53e+02 ... (remaining 129939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 52212 35.95 - 71.90: 4278 71.90 - 107.85: 548 107.85 - 143.81: 19 143.81 - 179.76: 36 Dihedral angle restraints: 57093 sinusoidal: 40971 harmonic: 16122 Sorted by residual: dihedral pdb=" CA ALA B 373 " pdb=" C ALA B 373 " pdb=" N VAL B 374 " pdb=" CA VAL B 374 " ideal model delta harmonic sigma weight residual -180.00 -57.89 -122.11 0 5.00e+00 4.00e-02 5.96e+02 dihedral pdb=" CA THR A 185 " pdb=" C THR A 185 " pdb=" N PRO A 186 " pdb=" CA PRO A 186 " ideal model delta harmonic sigma weight residual -180.00 -62.48 -117.52 0 5.00e+00 4.00e-02 5.52e+02 dihedral pdb=" CA ASP B 285 " pdb=" C ASP B 285 " pdb=" N ASP B 286 " pdb=" CA ASP B 286 " ideal model delta harmonic sigma weight residual 180.00 63.80 116.20 0 5.00e+00 4.00e-02 5.40e+02 ... (remaining 57090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 16042 1.006 - 2.011: 1 2.011 - 3.017: 0 3.017 - 4.023: 1 4.023 - 5.029: 4 Chirality restraints: 16048 Sorted by residual: chirality pdb=" C4' C4J 21244 " pdb=" C5' C4J 21244 " pdb=" O4' C4J 21244 " pdb=" C3' C4J 21244 " both_signs ideal model delta sigma weight residual False 2.50 -2.53 5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C3' G 3 65 " pdb=" C4' G 3 65 " pdb=" O3' G 3 65 " pdb=" C2' G 3 65 " both_signs ideal model delta sigma weight residual False -2.48 2.48 -4.95 2.00e-01 2.50e+01 6.13e+02 chirality pdb=" C2' C 1 17 " pdb=" C3' C 1 17 " pdb=" O2' C 1 17 " pdb=" C1' C 1 17 " both_signs ideal model delta sigma weight residual False -2.52 2.05 -4.57 2.00e-01 2.50e+01 5.21e+02 ... (remaining 16045 not shown) Planarity restraints: 9628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 21547 " -0.162 2.00e-02 2.50e+03 1.21e-01 4.38e+02 pdb=" N9 G 21547 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G 21547 " 0.184 2.00e-02 2.50e+03 pdb=" N7 G 21547 " 0.177 2.00e-02 2.50e+03 pdb=" C5 G 21547 " 0.015 2.00e-02 2.50e+03 pdb=" C6 G 21547 " -0.087 2.00e-02 2.50e+03 pdb=" O6 G 21547 " -0.165 2.00e-02 2.50e+03 pdb=" N1 G 21547 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G 21547 " 0.024 2.00e-02 2.50e+03 pdb=" N2 G 21547 " 0.183 2.00e-02 2.50e+03 pdb=" N3 G 21547 " -0.113 2.00e-02 2.50e+03 pdb=" C4 G 21547 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 869 " -0.190 2.00e-02 2.50e+03 1.04e-01 3.28e+02 pdb=" N9 G 2 869 " -0.023 2.00e-02 2.50e+03 pdb=" C8 G 2 869 " 0.102 2.00e-02 2.50e+03 pdb=" N7 G 2 869 " 0.154 2.00e-02 2.50e+03 pdb=" C5 G 2 869 " 0.073 2.00e-02 2.50e+03 pdb=" C6 G 2 869 " -0.069 2.00e-02 2.50e+03 pdb=" O6 G 2 869 " -0.122 2.00e-02 2.50e+03 pdb=" N1 G 2 869 " -0.114 2.00e-02 2.50e+03 pdb=" C2 G 2 869 " 0.011 2.00e-02 2.50e+03 pdb=" N2 G 2 869 " 0.145 2.00e-02 2.50e+03 pdb=" N3 G 2 869 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G 2 869 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 21170 " -0.126 2.00e-02 2.50e+03 1.09e-01 2.69e+02 pdb=" N1 U 21170 " 0.050 2.00e-02 2.50e+03 pdb=" C2 U 21170 " 0.070 2.00e-02 2.50e+03 pdb=" O2 U 21170 " -0.090 2.00e-02 2.50e+03 pdb=" N3 U 21170 " 0.186 2.00e-02 2.50e+03 pdb=" C4 U 21170 " 0.018 2.00e-02 2.50e+03 pdb=" O4 U 21170 " -0.194 2.00e-02 2.50e+03 pdb=" C5 U 21170 " 0.038 2.00e-02 2.50e+03 pdb=" C6 U 21170 " 0.048 2.00e-02 2.50e+03 ... (remaining 9625 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.42: 11 1.42 - 2.29: 78 2.29 - 3.16: 63391 3.16 - 4.03: 241353 4.03 - 4.90: 401173 Warning: very small nonbonded interaction distances. Nonbonded interactions: 706006 Sorted by model distance: nonbonded pdb=" O LYS J 107 " pdb=" O4' G 2 740 " model vdw 0.554 3.040 nonbonded pdb=" CB ARG J 106 " pdb=" O6 G 2 794 " model vdw 0.770 3.440 nonbonded pdb=" N ARG J 109 " pdb=" O2' G 2 740 " model vdw 0.900 2.520 nonbonded pdb=" N2 G 2 686 " pdb=" N4 C 2 729 " model vdw 0.950 3.200 nonbonded pdb=" O LYS J 107 " pdb=" C4' G 2 740 " model vdw 1.067 3.470 ... (remaining 706001 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 13.950 Check model and map are aligned: 0.930 Set scattering table: 0.600 Process input model: 218.830 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 243.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 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 : 0.018 0.522 89672 Z= 1.117 Angle : 2.025 60.605 129944 Z= 1.217 Chirality : 0.133 5.029 16048 Planarity : 0.020 0.178 9628 Dihedral : 21.633 179.758 46694 Min Nonbonded Distance : 0.554 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 3.58 % Allowed : 9.04 % Favored : 87.39 % Rotamer: Outliers : 1.68 % Allowed : 5.20 % Favored : 93.13 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.39 % Twisted Proline : 2.24 % Twisted General : 0.62 % 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: -4.09 (0.09), residues: 5534 helix: -2.68 (0.10), residues: 1548 sheet: -2.43 (0.15), residues: 950 loop : -2.87 (0.09), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.111 0.014 TRP g 247 HIS 0.006 0.001 HIS a 29 PHE 0.084 0.011 PHE J 87 TYR 0.174 0.018 TYR h 109 ARG 0.007 0.001 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1875 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1794 time to evaluate : 4.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ARG cc_start: 0.6292 (ttt-90) cc_final: 0.6075 (ttp80) REVERT: D 133 TYR cc_start: 0.7618 (m-80) cc_final: 0.7380 (m-80) REVERT: F 150 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.6057 (mtm) REVERT: I 162 LEU cc_start: 0.4648 (tp) cc_final: 0.4351 (tp) REVERT: K 67 TRP cc_start: 0.6315 (t60) cc_final: 0.6036 (t60) REVERT: L 146 SER cc_start: 0.7839 (m) cc_final: 0.7543 (p) REVERT: M 58 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7751 (m) REVERT: X 69 ILE cc_start: 0.7994 (mm) cc_final: 0.7694 (mt) REVERT: Z 105 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6059 (t80) REVERT: a 28 LEU cc_start: 0.7410 (mt) cc_final: 0.7183 (mt) REVERT: e 25 SER cc_start: 0.7524 (t) cc_final: 0.7245 (t) REVERT: g 305 ASN cc_start: 0.7034 (m-40) cc_final: 0.6812 (m-40) REVERT: U 144 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.3534 (ppt90) REVERT: R 137 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.5839 (m-70) outliers start: 81 outliers final: 14 residues processed: 1843 average time/residue: 0.9169 time to fit residues: 2703.9650 Evaluate side-chains 981 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 962 time to evaluate : 4.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain S residue 131 LYS Chi-restraints excluded: chain Z residue 105 PHE Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 615 optimal weight: 3.9990 chunk 552 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 372 optimal weight: 0.8980 chunk 295 optimal weight: 0.9980 chunk 571 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 425 optimal weight: 2.9990 chunk 662 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN D 101 HIS D 149 GLN D 158 HIS D 163 GLN E 98 GLN F 207 HIS G 50 ASN G 112 HIS G 201 HIS ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 ASN H 179 ASN I 59 GLN I 81 HIS I 186 GLN J 39 GLN ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN J 165 ASN J 186 ASN K 7 ASN L 154 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 13 GLN N 106 HIS N 112 HIS ** P 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 GLN Q 26 ASN S 114 GLN V 11 GLN W 81 GLN ** X 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 82 GLN Z 73 GLN b 17 HIS d 29 GLN e 4 GLN e 10 HIS e 16 GLN f 135 HIS g 62 HIS g 181 ASN g 285 GLN g 296 GLN h 103 HIS h 112 ASN i 111 GLN i 113 ASN B 62 HIS B 65 HIS B 78 HIS B 160 ASN B 180 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN U 11 HIS U 125 HIS U 134 GLN R 41 GLN R 79 HIS ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 89672 Z= 0.220 Angle : 0.751 12.964 129944 Z= 0.386 Chirality : 0.041 0.328 16048 Planarity : 0.006 0.092 9628 Dihedral : 22.591 179.061 35235 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.19 % Favored : 92.27 % Rotamer: Outliers : 3.77 % Allowed : 14.55 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.35 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.10), residues: 5534 helix: -0.96 (0.12), residues: 1538 sheet: -1.48 (0.16), residues: 917 loop : -2.46 (0.10), residues: 3079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 25 HIS 0.012 0.001 HIS X 76 PHE 0.020 0.002 PHE J 87 TYR 0.040 0.002 TYR P 38 ARG 0.009 0.001 ARG g 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1037 time to evaluate : 4.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 ARG cc_start: 0.6792 (ttt-90) cc_final: 0.6566 (ttp80) REVERT: F 148 LYS cc_start: 0.6953 (pptt) cc_final: 0.5848 (pptt) REVERT: F 166 TYR cc_start: 0.7056 (m-10) cc_final: 0.6589 (m-10) REVERT: G 139 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7646 (tp) REVERT: H 39 ILE cc_start: 0.7086 (mm) cc_final: 0.6767 (mm) REVERT: H 176 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7675 (tp30) REVERT: L 138 ARG cc_start: 0.7766 (ttm-80) cc_final: 0.7466 (ttp-170) REVERT: M 1 MET cc_start: 0.6403 (ptm) cc_final: 0.5808 (ptm) REVERT: P 45 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7787 (mp) REVERT: T 80 ARG cc_start: 0.6920 (ttt-90) cc_final: 0.6651 (ttp80) REVERT: V 36 THR cc_start: 0.8323 (t) cc_final: 0.8104 (t) REVERT: Z 95 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6606 (mt-10) REVERT: a 86 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6747 (tp30) REVERT: b 33 ASP cc_start: 0.8025 (p0) cc_final: 0.7761 (p0) REVERT: c 5 LYS cc_start: 0.6909 (mmmt) cc_final: 0.6583 (mmmt) REVERT: f 104 LYS cc_start: 0.5419 (OUTLIER) cc_final: 0.4952 (mtpp) REVERT: g 7 LEU cc_start: 0.6235 (tt) cc_final: 0.6012 (tp) REVERT: g 209 SER cc_start: 0.6994 (OUTLIER) cc_final: 0.6739 (p) REVERT: A 30 MET cc_start: 0.1866 (ptt) cc_final: 0.1634 (mmt) REVERT: U 15 VAL cc_start: 0.6828 (p) cc_final: 0.6578 (t) REVERT: U 144 ARG cc_start: 0.5827 (OUTLIER) cc_final: 0.3514 (ptp90) REVERT: R 41 GLN cc_start: 0.5187 (tt0) cc_final: 0.4949 (mm-40) REVERT: R 72 LYS cc_start: 0.5939 (pmtt) cc_final: 0.5399 (mmtp) REVERT: R 83 MET cc_start: 0.4543 (mtm) cc_final: 0.4004 (mtm) REVERT: R 137 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.5743 (m-70) outliers start: 182 outliers final: 93 residues processed: 1141 average time/residue: 0.9031 time to fit residues: 1737.9724 Evaluate side-chains 942 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 843 time to evaluate : 4.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain S residue 24 HIS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain W residue 83 ARG Chi-restraints excluded: chain W residue 92 HIS Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 80 SER Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 82 THR Chi-restraints excluded: chain Z residue 115 ILE Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 104 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain g residue 209 SER Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 367 optimal weight: 0.9990 chunk 205 optimal weight: 8.9990 chunk 550 optimal weight: 9.9990 chunk 450 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 663 optimal weight: 20.0000 chunk 716 optimal weight: 6.9990 chunk 590 optimal weight: 7.9990 chunk 657 optimal weight: 30.0000 chunk 226 optimal weight: 0.7980 chunk 532 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN F 174 HIS G 17 HIS G 67 GLN H 79 HIS H 83 ASN H 95 HIS I 59 GLN I 81 HIS ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN J 162 GLN J 186 ASN K 7 ASN K 22 HIS K 64 ASN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS N 5 GLN ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 HIS ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 ASN a 106 GLN b 80 HIS e 37 ASN g 159 ASN ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 45 ASN h 103 HIS ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 ASN A 60 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 89672 Z= 0.363 Angle : 0.817 14.044 129944 Z= 0.419 Chirality : 0.046 0.326 16048 Planarity : 0.007 0.107 9628 Dihedral : 22.517 179.316 35212 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.13 % Favored : 91.42 % Rotamer: Outliers : 5.28 % Allowed : 16.79 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.35 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.10), residues: 5534 helix: -0.62 (0.12), residues: 1585 sheet: -1.00 (0.16), residues: 1010 loop : -2.42 (0.10), residues: 2939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP P 25 HIS 0.030 0.002 HIS g 188 PHE 0.051 0.003 PHE c 79 TYR 0.037 0.003 TYR P 38 ARG 0.015 0.001 ARG P 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 919 time to evaluate : 4.888 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: C 50 ASN cc_start: 0.8257 (t0) cc_final: 0.7787 (t0) REVERT: E 105 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7545 (mm-40) REVERT: F 47 GLU cc_start: 0.7248 (mp0) cc_final: 0.6629 (mt-10) REVERT: G 80 ILE cc_start: 0.8391 (mp) cc_final: 0.8186 (mp) REVERT: G 87 MET cc_start: 0.6120 (mmm) cc_final: 0.5775 (mmm) REVERT: G 139 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8152 (tp) REVERT: H 124 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6605 (m-30) REVERT: K 88 ASN cc_start: 0.7572 (t0) cc_final: 0.7207 (t0) REVERT: L 13 TYR cc_start: 0.8467 (p90) cc_final: 0.8236 (p90) REVERT: L 138 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7538 (ttp-170) REVERT: M 1 MET cc_start: 0.6560 (ptm) cc_final: 0.5899 (ptm) REVERT: M 7 ASN cc_start: 0.7444 (m110) cc_final: 0.7198 (m110) REVERT: V 10 ASN cc_start: 0.7441 (t0) cc_final: 0.6663 (t0) REVERT: X 18 SER cc_start: 0.8130 (p) cc_final: 0.7866 (m) REVERT: Z 1 MET cc_start: 0.0327 (OUTLIER) cc_final: -0.0955 (mmt) REVERT: Z 95 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6423 (mt-10) REVERT: b 5 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8485 (mmt90) REVERT: d 60 GLU cc_start: 0.6535 (pt0) cc_final: 0.6333 (pt0) REVERT: g 52 TYR cc_start: 0.5827 (t80) cc_final: 0.5586 (t80) REVERT: g 191 HIS cc_start: 0.5876 (OUTLIER) cc_final: 0.5206 (m170) REVERT: g 218 LEU cc_start: 0.7165 (mm) cc_final: 0.6900 (mp) REVERT: h 101 SER cc_start: 0.7889 (t) cc_final: 0.7637 (t) REVERT: i 116 PHE cc_start: 0.7830 (m-10) cc_final: 0.7607 (m-80) REVERT: A 45 MET cc_start: 0.5158 (ttm) cc_final: 0.4134 (ttm) REVERT: A 80 LYS cc_start: 0.6156 (mtmt) cc_final: 0.5106 (mmtt) REVERT: A 223 MET cc_start: 0.1046 (tmm) cc_final: -0.0336 (tpt) REVERT: U 111 LEU cc_start: 0.5579 (OUTLIER) cc_final: 0.5039 (mp) REVERT: U 126 PHE cc_start: 0.7542 (t80) cc_final: 0.7088 (t80) REVERT: U 144 ARG cc_start: 0.5587 (OUTLIER) cc_final: 0.3432 (ptp90) REVERT: R 53 GLN cc_start: 0.6606 (OUTLIER) cc_final: 0.6171 (tp40) REVERT: R 137 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.5911 (m-70) outliers start: 255 outliers final: 145 residues processed: 1084 average time/residue: 0.8133 time to fit residues: 1490.6150 Evaluate side-chains 910 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 756 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 7 TRP Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 24 HIS Chi-restraints excluded: chain S residue 49 TYR Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 115 TYR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 69 ILE Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain W residue 78 ASP Chi-restraints excluded: chain W residue 83 ARG Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain b residue 5 ARG Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 55 LEU Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain g residue 40 ILE Chi-restraints excluded: chain g residue 96 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 261 LEU Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 96 LEU Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 111 LEU Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 28 MET Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 655 optimal weight: 9.9990 chunk 498 optimal weight: 10.0000 chunk 344 optimal weight: 0.9990 chunk 73 optimal weight: 0.0170 chunk 316 optimal weight: 1.9990 chunk 445 optimal weight: 7.9990 chunk 665 optimal weight: 8.9990 chunk 704 optimal weight: 3.9990 chunk 347 optimal weight: 2.9990 chunk 630 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 111 GLN C 113 GLN F 74 GLN F 174 HIS ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 HIS ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 GLN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 GLN P 62 GLN P 101 HIS Q 26 ASN S 142 GLN a 19 GLN a 89 HIS ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 HIS ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 296 GLN h 89 GLN ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 42 HIS ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 120 HIS R 41 GLN ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 89672 Z= 0.226 Angle : 0.653 14.161 129944 Z= 0.336 Chirality : 0.040 0.328 16048 Planarity : 0.005 0.094 9628 Dihedral : 22.360 178.712 35208 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.96 % Favored : 92.65 % Rotamer: Outliers : 4.64 % Allowed : 18.80 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.35 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.10), residues: 5534 helix: -0.16 (0.13), residues: 1567 sheet: -0.80 (0.16), residues: 1001 loop : -2.31 (0.10), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP g 219 HIS 0.013 0.001 HIS g 188 PHE 0.023 0.002 PHE H 20 TYR 0.046 0.002 TYR P 38 ARG 0.007 0.001 ARG i 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 817 time to evaluate : 4.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7897 (t0) REVERT: E 105 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7457 (mm-40) REVERT: F 47 GLU cc_start: 0.7233 (mp0) cc_final: 0.6852 (mt-10) REVERT: F 90 LYS cc_start: 0.6785 (tttm) cc_final: 0.6548 (tttm) REVERT: F 166 TYR cc_start: 0.6718 (m-10) cc_final: 0.6450 (m-10) REVERT: H 123 GLU cc_start: 0.7433 (pt0) cc_final: 0.7225 (pt0) REVERT: I 43 GLU cc_start: 0.5692 (OUTLIER) cc_final: 0.5303 (pm20) REVERT: I 162 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5439 (mp) REVERT: K 88 ASN cc_start: 0.7600 (t0) cc_final: 0.7190 (t0) REVERT: M 1 MET cc_start: 0.6456 (ptm) cc_final: 0.5850 (ptm) REVERT: M 35 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6444 (mm) REVERT: M 58 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7596 (t) REVERT: P 26 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7211 (tt) REVERT: P 45 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8181 (mp) REVERT: P 119 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8235 (tp30) REVERT: X 18 SER cc_start: 0.8256 (p) cc_final: 0.7942 (m) REVERT: X 52 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7900 (p) REVERT: g 218 LEU cc_start: 0.7082 (mm) cc_final: 0.6871 (mp) REVERT: i 116 PHE cc_start: 0.7841 (m-10) cc_final: 0.7570 (m-80) REVERT: A 80 LYS cc_start: 0.6121 (mtmt) cc_final: 0.5078 (mmtt) REVERT: A 154 LYS cc_start: -0.0059 (mmmt) cc_final: -0.0979 (ptpt) REVERT: A 223 MET cc_start: 0.1190 (tmm) cc_final: -0.0644 (tpt) REVERT: U 61 GLU cc_start: 0.6851 (pm20) cc_final: 0.6425 (pm20) REVERT: U 117 ILE cc_start: 0.7555 (pt) cc_final: 0.7354 (pt) REVERT: U 126 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7078 (t80) REVERT: U 144 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.3424 (ptp90) REVERT: R 137 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.6010 (m-70) outliers start: 224 outliers final: 134 residues processed: 967 average time/residue: 0.7854 time to fit residues: 1302.0775 Evaluate side-chains 901 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 755 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 43 GLU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 76 GLN Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain S residue 24 HIS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 115 TYR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain X residue 8 PHE Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain a residue 18 LEU Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain g residue 104 HIS Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 90 GLU Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 126 PHE Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 28 MET Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 586 optimal weight: 6.9990 chunk 400 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 524 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 601 optimal weight: 10.0000 chunk 487 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 359 optimal weight: 1.9990 chunk 632 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 111 GLN C 132 GLN C 164 ASN F 74 GLN F 174 HIS G 138 HIS ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 GLN ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 HIS S 142 GLN X 76 HIS ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 132 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 41 GLN ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 89672 Z= 0.336 Angle : 0.723 12.871 129944 Z= 0.368 Chirality : 0.043 0.265 16048 Planarity : 0.006 0.093 9628 Dihedral : 22.373 179.363 35204 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.42 % Favored : 91.22 % Rotamer: Outliers : 5.90 % Allowed : 18.63 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.35 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.11), residues: 5534 helix: -0.23 (0.13), residues: 1582 sheet: -0.80 (0.16), residues: 1015 loop : -2.34 (0.10), residues: 2937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 219 HIS 0.012 0.002 HIS e 28 PHE 0.029 0.002 PHE H 20 TYR 0.038 0.002 TYR P 38 ARG 0.016 0.001 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 784 time to evaluate : 4.847 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 186 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.5561 (ptm160) REVERT: E 105 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7308 (mm-40) REVERT: E 137 ARG cc_start: 0.7209 (ttp-110) cc_final: 0.6976 (mtm180) REVERT: J 32 MET cc_start: 0.5231 (ppp) cc_final: 0.4140 (tpp) REVERT: K 10 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7747 (ptmt) REVERT: K 88 ASN cc_start: 0.7869 (t0) cc_final: 0.7440 (t0) REVERT: L 102 ILE cc_start: 0.8779 (mm) cc_final: 0.8531 (mt) REVERT: M 1 MET cc_start: 0.6377 (ptm) cc_final: 0.6067 (ptm) REVERT: M 58 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7725 (t) REVERT: P 26 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7436 (tt) REVERT: T 1 MET cc_start: 0.2211 (mmp) cc_final: 0.1960 (mmp) REVERT: V 10 ASN cc_start: 0.7320 (t0) cc_final: 0.6718 (t0) REVERT: X 21 ASN cc_start: 0.8725 (t0) cc_final: 0.8277 (t0) REVERT: b 5 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8486 (mmt90) REVERT: b 33 ASP cc_start: 0.8305 (p0) cc_final: 0.7916 (p0) REVERT: c 82 LYS cc_start: 0.6324 (OUTLIER) cc_final: 0.5791 (pttm) REVERT: g 113 PHE cc_start: 0.5972 (OUTLIER) cc_final: 0.5681 (t80) REVERT: g 218 LEU cc_start: 0.7354 (mm) cc_final: 0.7022 (mp) REVERT: h 65 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.5664 (m-10) REVERT: i 116 PHE cc_start: 0.7904 (m-10) cc_final: 0.7632 (m-80) REVERT: A 45 MET cc_start: 0.5016 (ttt) cc_final: 0.4338 (ttm) REVERT: A 64 ARG cc_start: 0.1173 (OUTLIER) cc_final: -0.0772 (pmt100) REVERT: A 80 LYS cc_start: 0.6575 (mtmt) cc_final: 0.5554 (mmtt) REVERT: A 223 MET cc_start: 0.1731 (tmm) cc_final: 0.0088 (tpt) REVERT: U 126 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7179 (t80) REVERT: U 144 ARG cc_start: 0.5485 (OUTLIER) cc_final: 0.3123 (ppt90) REVERT: R 137 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6065 (m-70) outliers start: 285 outliers final: 195 residues processed: 984 average time/residue: 0.7652 time to fit residues: 1298.4568 Evaluate side-chains 943 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 736 time to evaluate : 4.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 16 ILE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 LYS Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 76 GLN Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 6 ASP Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain L residue 7 TRP Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 3 MET Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain S residue 24 HIS Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 115 TYR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 65 THR Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 115 ILE Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain a residue 18 LEU Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 5 ARG Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 54 SER Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain c residue 82 LYS Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 140 TYR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain g residue 196 ASN Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain h residue 56 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 65 TYR Chi-restraints excluded: chain h residue 96 LEU Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 82 ARG Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 126 PHE Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 28 MET Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 237 optimal weight: 0.9990 chunk 634 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 413 optimal weight: 1.9990 chunk 173 optimal weight: 0.0980 chunk 705 optimal weight: 4.9990 chunk 585 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 233 optimal weight: 0.6980 chunk 370 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 GLN F 174 HIS ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN L 113 GLN L 156 HIS P 62 GLN S 142 GLN Z 77 ASN c 26 GLN ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 112 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 89672 Z= 0.156 Angle : 0.601 14.037 129944 Z= 0.307 Chirality : 0.037 0.251 16048 Planarity : 0.005 0.090 9628 Dihedral : 22.275 178.246 35202 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.14 % Favored : 92.56 % Rotamer: Outliers : 3.87 % Allowed : 21.01 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.11), residues: 5534 helix: 0.14 (0.13), residues: 1580 sheet: -0.72 (0.16), residues: 1009 loop : -2.21 (0.10), residues: 2945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 219 HIS 0.013 0.001 HIS e 28 PHE 0.021 0.001 PHE V 14 TYR 0.043 0.001 TYR P 38 ARG 0.006 0.000 ARG X 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 819 time to evaluate : 5.311 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 186 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.5462 (ptm160) REVERT: E 137 ARG cc_start: 0.7141 (ttp-110) cc_final: 0.6936 (mtm180) REVERT: F 166 TYR cc_start: 0.6336 (m-10) cc_final: 0.6111 (m-10) REVERT: J 32 MET cc_start: 0.5355 (ppp) cc_final: 0.4278 (tpp) REVERT: J 153 LEU cc_start: 0.8219 (tt) cc_final: 0.8014 (tt) REVERT: J 181 THR cc_start: 0.8473 (p) cc_final: 0.8272 (p) REVERT: K 88 ASN cc_start: 0.7842 (t0) cc_final: 0.7305 (t0) REVERT: L 154 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7501 (tm-30) REVERT: M 1 MET cc_start: 0.6465 (ptm) cc_final: 0.6160 (ptm) REVERT: P 26 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7240 (tt) REVERT: Q 91 THR cc_start: 0.7268 (p) cc_final: 0.6925 (m) REVERT: T 1 MET cc_start: 0.2031 (mmp) cc_final: 0.1715 (mmp) REVERT: T 73 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8374 (tt) REVERT: W 78 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7686 (t0) REVERT: X 21 ASN cc_start: 0.8649 (t0) cc_final: 0.8214 (t0) REVERT: Z 1 MET cc_start: 0.0179 (mmt) cc_final: -0.0220 (mmt) REVERT: b 5 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8265 (mmt90) REVERT: b 33 ASP cc_start: 0.8118 (p0) cc_final: 0.7778 (p0) REVERT: c 14 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6449 (tm-30) REVERT: c 15 GLU cc_start: 0.7144 (tp30) cc_final: 0.6869 (mm-30) REVERT: c 55 LEU cc_start: 0.7158 (mm) cc_final: 0.6821 (mt) REVERT: e 54 LYS cc_start: 0.8327 (mttm) cc_final: 0.7806 (mtpt) REVERT: i 116 PHE cc_start: 0.7725 (m-10) cc_final: 0.7519 (m-80) REVERT: A 45 MET cc_start: 0.5164 (ttt) cc_final: 0.4892 (ttm) REVERT: A 80 LYS cc_start: 0.6427 (mtmt) cc_final: 0.5412 (mmtt) REVERT: A 223 MET cc_start: 0.1441 (tmm) cc_final: -0.0109 (tpt) REVERT: B 421 ILE cc_start: -0.1687 (OUTLIER) cc_final: -0.2087 (tt) REVERT: U 126 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7175 (t80) REVERT: U 144 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.3474 (ptp90) REVERT: R 137 HIS cc_start: 0.6669 (OUTLIER) cc_final: 0.5919 (m-70) outliers start: 187 outliers final: 123 residues processed: 941 average time/residue: 0.8301 time to fit residues: 1346.5339 Evaluate side-chains 874 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 742 time to evaluate : 4.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 204 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 201 LYS Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain L residue 7 TRP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 131 CYS Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 142 GLU Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain S residue 24 HIS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 73 LEU Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain W residue 78 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 115 ILE Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 5 ARG Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 126 PHE Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 28 MET Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 680 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 401 optimal weight: 0.7980 chunk 515 optimal weight: 20.0000 chunk 399 optimal weight: 0.7980 chunk 593 optimal weight: 8.9990 chunk 393 optimal weight: 0.0270 chunk 702 optimal weight: 3.9990 chunk 439 optimal weight: 2.9990 chunk 428 optimal weight: 10.0000 chunk 324 optimal weight: 0.2980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 GLN F 174 HIS ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 GLN M 7 ASN S 142 GLN a 19 GLN c 26 GLN ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 HIS ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 89672 Z= 0.155 Angle : 0.581 14.030 129944 Z= 0.297 Chirality : 0.036 0.237 16048 Planarity : 0.005 0.086 9628 Dihedral : 22.200 178.336 35202 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.26 % Favored : 92.46 % Rotamer: Outliers : 4.00 % Allowed : 21.65 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.35 % 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: -1.65 (0.11), residues: 5534 helix: 0.31 (0.13), residues: 1584 sheet: -0.62 (0.16), residues: 1016 loop : -2.14 (0.10), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 45 HIS 0.013 0.001 HIS e 28 PHE 0.026 0.001 PHE G 86 TYR 0.044 0.001 TYR P 38 ARG 0.027 0.000 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 788 time to evaluate : 4.877 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: C 186 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.5418 (ptm160) REVERT: D 148 ASN cc_start: 0.5169 (m-40) cc_final: 0.4822 (m-40) REVERT: I 162 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5384 (mp) REVERT: I 217 MET cc_start: 0.5090 (tpp) cc_final: 0.4868 (tpt) REVERT: K 88 ASN cc_start: 0.7816 (t0) cc_final: 0.7228 (t0) REVERT: L 154 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7550 (tm-30) REVERT: M 1 MET cc_start: 0.6405 (ptm) cc_final: 0.5850 (ptm) REVERT: M 8 ARG cc_start: 0.7445 (tpp-160) cc_final: 0.7091 (ttm-80) REVERT: Q 91 THR cc_start: 0.7326 (p) cc_final: 0.6982 (m) REVERT: T 1 MET cc_start: 0.2297 (mmp) cc_final: 0.1930 (mmp) REVERT: T 119 VAL cc_start: 0.6456 (p) cc_final: 0.6128 (t) REVERT: T 126 MET cc_start: 0.4243 (tpp) cc_final: 0.3953 (mtt) REVERT: X 21 ASN cc_start: 0.8646 (t0) cc_final: 0.8194 (t0) REVERT: b 5 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8184 (mmt90) REVERT: b 33 ASP cc_start: 0.8144 (p0) cc_final: 0.7875 (p0) REVERT: c 55 LEU cc_start: 0.7113 (mm) cc_final: 0.6753 (mt) REVERT: c 82 LYS cc_start: 0.5621 (pttm) cc_final: 0.5257 (pttm) REVERT: g 37 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7134 (p0) REVERT: i 116 PHE cc_start: 0.7787 (m-10) cc_final: 0.7517 (m-80) REVERT: A 45 MET cc_start: 0.4945 (ttt) cc_final: 0.4576 (ttm) REVERT: A 80 LYS cc_start: 0.6468 (mtmt) cc_final: 0.5387 (mmtt) REVERT: A 223 MET cc_start: 0.1381 (OUTLIER) cc_final: -0.0078 (tpt) REVERT: U 126 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7203 (t80) REVERT: U 144 ARG cc_start: 0.5296 (OUTLIER) cc_final: 0.3552 (ptp90) REVERT: R 137 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.5959 (m-70) outliers start: 193 outliers final: 130 residues processed: 916 average time/residue: 0.8364 time to fit residues: 1319.3185 Evaluate side-chains 881 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 743 time to evaluate : 4.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 201 LYS Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain L residue 7 TRP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LYS Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain S residue 24 HIS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain X residue 8 PHE Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 115 ILE Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 5 ARG Chi-restraints excluded: chain b residue 29 CYS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 37 ASP Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain U residue 11 HIS Chi-restraints excluded: chain U residue 30 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 126 PHE Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 28 MET Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 434 optimal weight: 9.9990 chunk 280 optimal weight: 0.9990 chunk 419 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 446 optimal weight: 0.0970 chunk 478 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 552 optimal weight: 6.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 GLN F 174 HIS ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 ASN N 11 GLN S 80 GLN S 114 GLN S 142 GLN Z 23 HIS d 45 ASN ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 89672 Z= 0.292 Angle : 0.677 15.092 129944 Z= 0.344 Chirality : 0.041 0.334 16048 Planarity : 0.005 0.087 9628 Dihedral : 22.249 179.226 35202 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.26 % Favored : 91.51 % Rotamer: Outliers : 4.31 % Allowed : 21.76 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.35 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.11), residues: 5534 helix: 0.12 (0.13), residues: 1589 sheet: -0.61 (0.16), residues: 1011 loop : -2.20 (0.10), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 45 HIS 0.037 0.002 HIS U 11 PHE 0.035 0.002 PHE G 86 TYR 0.036 0.002 TYR P 38 ARG 0.023 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 772 time to evaluate : 4.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.5617 (ptm160) REVERT: F 1 MET cc_start: 0.2160 (OUTLIER) cc_final: 0.1903 (mpt) REVERT: H 102 LEU cc_start: 0.8351 (tt) cc_final: 0.8122 (tp) REVERT: I 5 ILE cc_start: 0.7584 (mm) cc_final: 0.7307 (mm) REVERT: I 217 MET cc_start: 0.5382 (tpp) cc_final: 0.5143 (tpt) REVERT: K 78 ILE cc_start: 0.8596 (mp) cc_final: 0.8137 (mt) REVERT: K 88 ASN cc_start: 0.7920 (t0) cc_final: 0.7293 (t0) REVERT: L 102 ILE cc_start: 0.8705 (mm) cc_final: 0.8447 (mt) REVERT: L 154 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7573 (tm-30) REVERT: M 1 MET cc_start: 0.6357 (ptm) cc_final: 0.5851 (ptm) REVERT: M 58 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7608 (t) REVERT: Q 91 THR cc_start: 0.7406 (p) cc_final: 0.7098 (m) REVERT: T 119 VAL cc_start: 0.6509 (p) cc_final: 0.6231 (t) REVERT: X 21 ASN cc_start: 0.8695 (t0) cc_final: 0.8185 (t0) REVERT: X 22 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7432 (ptp-170) REVERT: b 5 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8472 (mmt90) REVERT: b 33 ASP cc_start: 0.8220 (p0) cc_final: 0.7897 (p0) REVERT: c 55 LEU cc_start: 0.7134 (mm) cc_final: 0.6776 (mt) REVERT: i 116 PHE cc_start: 0.7888 (m-10) cc_final: 0.7607 (m-80) REVERT: A 45 MET cc_start: 0.4830 (ttt) cc_final: 0.4086 (ttm) REVERT: A 64 ARG cc_start: 0.1030 (OUTLIER) cc_final: 0.0751 (pmt100) REVERT: A 80 LYS cc_start: 0.6949 (mtmt) cc_final: 0.5861 (mmtt) REVERT: A 223 MET cc_start: 0.0963 (OUTLIER) cc_final: -0.0413 (tpt) REVERT: U 126 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7208 (t80) REVERT: U 144 ARG cc_start: 0.5280 (OUTLIER) cc_final: 0.2809 (ppt90) REVERT: R 137 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.5983 (m-70) outliers start: 208 outliers final: 166 residues processed: 912 average time/residue: 0.7872 time to fit residues: 1227.4314 Evaluate side-chains 910 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 735 time to evaluate : 4.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 LYS Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 76 GLN Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain L residue 7 TRP Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LYS Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain S residue 24 HIS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 59 LYS Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain X residue 10 ASP Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 5 ARG Chi-restraints excluded: chain b residue 29 CYS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 28 HIS Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 157 SER Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain h residue 55 TYR Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 82 ARG Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 126 PHE Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 28 MET Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 639 optimal weight: 6.9990 chunk 673 optimal weight: 10.0000 chunk 614 optimal weight: 20.0000 chunk 654 optimal weight: 6.9990 chunk 672 optimal weight: 9.9990 chunk 394 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 514 optimal weight: 20.0000 chunk 200 optimal weight: 1.9990 chunk 591 optimal weight: 6.9990 chunk 619 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN D 95 ASN E 121 HIS F 74 GLN F 174 HIS ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 GLN N 141 ASN ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 ASN Z 73 GLN e 4 GLN ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 HIS A 23 ASN A 41 ASN ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 11 HIS ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.7127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 89672 Z= 0.438 Angle : 0.812 15.024 129944 Z= 0.410 Chirality : 0.047 0.284 16048 Planarity : 0.006 0.093 9628 Dihedral : 22.489 179.944 35202 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.69 % Favored : 90.10 % Rotamer: Outliers : 4.86 % Allowed : 21.65 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.79 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.11), residues: 5534 helix: -0.34 (0.13), residues: 1569 sheet: -0.72 (0.17), residues: 983 loop : -2.38 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 170 HIS 0.016 0.002 HIS U 11 PHE 0.033 0.002 PHE G 86 TYR 0.035 0.002 TYR P 38 ARG 0.015 0.001 ARG d 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 744 time to evaluate : 4.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.5704 (ptm160) REVERT: H 102 LEU cc_start: 0.8341 (tt) cc_final: 0.8049 (tp) REVERT: I 63 MET cc_start: 0.7522 (ptm) cc_final: 0.7319 (ptm) REVERT: J 149 ASP cc_start: 0.6488 (p0) cc_final: 0.6239 (p0) REVERT: K 10 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7630 (ptmt) REVERT: K 88 ASN cc_start: 0.8062 (t0) cc_final: 0.7408 (t0) REVERT: L 102 ILE cc_start: 0.8826 (mm) cc_final: 0.8541 (mt) REVERT: L 154 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7516 (tm-30) REVERT: M 1 MET cc_start: 0.6358 (ptm) cc_final: 0.6076 (ptm) REVERT: M 58 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7666 (t) REVERT: V 10 ASN cc_start: 0.6907 (t0) cc_final: 0.6237 (t0) REVERT: X 18 SER cc_start: 0.8540 (p) cc_final: 0.8167 (m) REVERT: X 21 ASN cc_start: 0.8725 (t0) cc_final: 0.8212 (t0) REVERT: X 22 ARG cc_start: 0.7674 (ptp90) cc_final: 0.7383 (ptp-170) REVERT: b 5 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8610 (mmt90) REVERT: b 33 ASP cc_start: 0.8346 (p0) cc_final: 0.8012 (p0) REVERT: d 64 GLU cc_start: 0.7377 (tp30) cc_final: 0.6976 (tp30) REVERT: g 5 MET cc_start: 0.4768 (mmt) cc_final: 0.4543 (mmt) REVERT: h 101 SER cc_start: 0.7740 (t) cc_final: 0.7459 (t) REVERT: i 116 PHE cc_start: 0.8003 (m-10) cc_final: 0.7737 (m-80) REVERT: A 45 MET cc_start: 0.4396 (ttt) cc_final: 0.3963 (ttm) REVERT: A 80 LYS cc_start: 0.7421 (mtmt) cc_final: 0.6276 (mmtt) REVERT: A 223 MET cc_start: 0.1513 (OUTLIER) cc_final: 0.0038 (tpt) REVERT: A 237 MET cc_start: 0.1397 (tmm) cc_final: -0.0591 (tpt) REVERT: U 144 ARG cc_start: 0.5383 (OUTLIER) cc_final: 0.2719 (ppt90) REVERT: R 53 GLN cc_start: 0.6928 (mm-40) cc_final: 0.6715 (mp10) REVERT: R 137 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6038 (m-70) outliers start: 235 outliers final: 189 residues processed: 910 average time/residue: 0.7817 time to fit residues: 1226.4176 Evaluate side-chains 904 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 708 time to evaluate : 4.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 LYS Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 76 GLN Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 7 TRP Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 173 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 38 LYS Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 38 ASN Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain S residue 24 HIS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 115 TYR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 118 GLN Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 90 SER Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain X residue 10 ASP Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain Y residue 23 ARG Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 115 ILE Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain a residue 42 GLU Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 5 ARG Chi-restraints excluded: chain b residue 29 CYS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain b residue 76 SER Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain b residue 94 ASP Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 28 HIS Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 157 SER Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 277 THR Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain h residue 55 TYR Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 67 LEU Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 82 ARG Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 69 THR Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 28 MET Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 652 optimal weight: 50.0000 chunk 429 optimal weight: 4.9990 chunk 692 optimal weight: 6.9990 chunk 422 optimal weight: 0.9980 chunk 328 optimal weight: 4.9990 chunk 481 optimal weight: 6.9990 chunk 726 optimal weight: 10.0000 chunk 668 optimal weight: 5.9990 chunk 578 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 446 optimal weight: 0.6980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN F 174 HIS ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 GLN ** S 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.7206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 89672 Z= 0.267 Angle : 0.683 17.274 129944 Z= 0.348 Chirality : 0.041 0.273 16048 Planarity : 0.005 0.088 9628 Dihedral : 22.382 179.369 35202 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.11 % Favored : 91.69 % Rotamer: Outliers : 4.12 % Allowed : 22.54 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.35 % Twisted General : 0.06 % 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: -1.98 (0.11), residues: 5534 helix: -0.04 (0.13), residues: 1551 sheet: -0.73 (0.17), residues: 992 loop : -2.31 (0.10), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 45 HIS 0.011 0.001 HIS e 28 PHE 0.030 0.002 PHE G 86 TYR 0.037 0.002 TYR P 38 ARG 0.021 0.001 ARG b 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11068 Ramachandran restraints generated. 5534 Oldfield, 0 Emsley, 5534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 731 time to evaluate : 6.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.5617 (ptm160) REVERT: H 102 LEU cc_start: 0.8233 (tt) cc_final: 0.7932 (tp) REVERT: I 217 MET cc_start: 0.5589 (tpp) cc_final: 0.5317 (tpt) REVERT: K 10 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7601 (ptmt) REVERT: K 88 ASN cc_start: 0.7983 (t0) cc_final: 0.7347 (t0) REVERT: L 102 ILE cc_start: 0.8767 (mm) cc_final: 0.8495 (mt) REVERT: L 154 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7544 (tm-30) REVERT: X 18 SER cc_start: 0.8441 (p) cc_final: 0.8090 (m) REVERT: X 21 ASN cc_start: 0.8729 (t0) cc_final: 0.8249 (t0) REVERT: X 22 ARG cc_start: 0.7684 (ptp90) cc_final: 0.7391 (ptp-170) REVERT: b 5 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8459 (mmt90) REVERT: b 33 ASP cc_start: 0.8174 (p0) cc_final: 0.7894 (p0) REVERT: d 64 GLU cc_start: 0.7287 (tp30) cc_final: 0.6899 (tp30) REVERT: i 93 VAL cc_start: 0.8724 (m) cc_final: 0.8498 (m) REVERT: i 116 PHE cc_start: 0.7886 (m-10) cc_final: 0.7593 (m-80) REVERT: A 45 MET cc_start: 0.4600 (ttt) cc_final: 0.4147 (ttm) REVERT: A 64 ARG cc_start: 0.1734 (OUTLIER) cc_final: 0.0542 (pmt100) REVERT: A 80 LYS cc_start: 0.7337 (mtmt) cc_final: 0.6099 (mmtt) REVERT: A 223 MET cc_start: 0.1447 (OUTLIER) cc_final: 0.0068 (tpt) REVERT: A 237 MET cc_start: 0.1456 (tmm) cc_final: -0.0509 (tpt) REVERT: U 144 ARG cc_start: 0.5317 (OUTLIER) cc_final: 0.2783 (ppt90) REVERT: R 53 GLN cc_start: 0.6824 (mm-40) cc_final: 0.6609 (mp10) REVERT: R 137 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.5990 (m-70) outliers start: 199 outliers final: 174 residues processed: 871 average time/residue: 0.7766 time to fit residues: 1174.3738 Evaluate side-chains 894 residues out of total 4831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 713 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 186 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 39 LYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 88 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 201 LYS Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 76 GLN Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 172 THR Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 91 VAL Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 159 SER Chi-restraints excluded: chain K residue 166 PHE Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 7 TRP Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 38 LYS Chi-restraints excluded: chain M residue 39 ASN Chi-restraints excluded: chain M residue 43 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain Q residue 36 SER Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain S residue 24 HIS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 76 GLU Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 97 GLU Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 118 GLN Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 85 ASN Chi-restraints excluded: chain V residue 134 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 59 LYS Chi-restraints excluded: chain W residue 74 SER Chi-restraints excluded: chain X residue 10 ASP Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 81 VAL Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Z residue 77 ASN Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 115 ILE Chi-restraints excluded: chain Z residue 119 ARG Chi-restraints excluded: chain a residue 42 GLU Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 5 ARG Chi-restraints excluded: chain b residue 29 CYS Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 72 HIS Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 86 ASN Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain d residue 23 SER Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 28 HIS Chi-restraints excluded: chain e residue 39 CYS Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 90 LYS Chi-restraints excluded: chain f residue 118 ARG Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 74 ASP Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 157 SER Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 186 THR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 289 LEU Chi-restraints excluded: chain h residue 55 TYR Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 67 LEU Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain i residue 82 ARG Chi-restraints excluded: chain i residue 83 VAL Chi-restraints excluded: chain i residue 110 MET Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 138 THR Chi-restraints excluded: chain U residue 144 ARG Chi-restraints excluded: chain R residue 28 MET Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 137 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 354 optimal weight: 0.5980 chunk 459 optimal weight: 5.9990 chunk 616 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 533 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 160 optimal weight: 0.3980 chunk 579 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 594 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN F 174 HIS ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 GLN ** S 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 ASN ** i 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.148537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.105704 restraints weight = 155331.756| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.81 r_work: 0.3136 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 89672 Z= 0.213 Angle : 0.635 17.126 129944 Z= 0.323 Chirality : 0.038 0.256 16048 Planarity : 0.005 0.088 9628 Dihedral : 22.291 178.966 35202 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.46 % Favored : 91.34 % Rotamer: Outliers : 3.79 % Allowed : 23.06 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.47 % Twisted Proline : 1.35 % Twisted General : 0.06 % 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: -1.84 (0.11), residues: 5534 helix: 0.14 (0.13), residues: 1572 sheet: -0.68 (0.17), residues: 997 loop : -2.26 (0.10), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 90 HIS 0.011 0.001 HIS e 28 PHE 0.033 0.001 PHE G 86 TYR 0.037 0.002 TYR P 38 ARG 0.010 0.001 ARG b 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22648.52 seconds wall clock time: 403 minutes 32.60 seconds (24212.60 seconds total)