Starting phenix.real_space_refine on Sun Feb 25 03:04:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adn_15365/02_2024/8adn_15365.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adn_15365/02_2024/8adn_15365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adn_15365/02_2024/8adn_15365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adn_15365/02_2024/8adn_15365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adn_15365/02_2024/8adn_15365.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adn_15365/02_2024/8adn_15365.pdb" } resolution = 2.77 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= 0.001 sd= 0.135 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: 4 Type Number sf(0) Gaussians S 246 5.16 5 C 30638 2.51 5 N 8052 2.21 5 O 9382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 128": "OD1" <-> "OD2" Residue "3 ASP 130": "OD1" <-> "OD2" Residue "3 ASP 132": "OD1" <-> "OD2" Residue "3 ASP 140": "OD1" <-> "OD2" Residue "3 ASP 142": "OD1" <-> "OD2" Residue "4 ASP 83": "OD1" <-> "OD2" Residue "4 ASP 84": "OD1" <-> "OD2" Residue "4 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 105": "OE1" <-> "OE2" Residue "4 ASP 116": "OD1" <-> "OD2" Residue "4 ASP 119": "OD1" <-> "OD2" Residue "4 ASP 132": "OD1" <-> "OD2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 41": "OD1" <-> "OD2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "F ASP 7": "OD1" <-> "OD2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F ASP 205": "OD1" <-> "OD2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G ASP 221": "OD1" <-> "OD2" Residue "H TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H ASP 45": "OD1" <-> "OD2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H ASP 179": "OD1" <-> "OD2" Residue "H GLU 189": "OE1" <-> "OE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "I ASP 26": "OD1" <-> "OD2" Residue "I ASP 82": "OD1" <-> "OD2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 160": "OD1" <-> "OD2" Residue "I GLU 161": "OE1" <-> "OE2" Residue "I ASP 178": "OD1" <-> "OD2" Residue "I ASP 205": "OD1" <-> "OD2" Residue "J ASP 33": "OD1" <-> "OD2" Residue "J PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 49": "OD1" <-> "OD2" Residue "J TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 126": "OD1" <-> "OD2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 48": "OD1" <-> "OD2" Residue "K PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "K ASP 147": "OD1" <-> "OD2" Residue "K ASP 177": "OD1" <-> "OD2" Residue "K GLU 181": "OE1" <-> "OE2" Residue "K PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 222": "OD1" <-> "OD2" Residue "L ASP 96": "OD1" <-> "OD2" Residue "L TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "L ASP 202": "OD1" <-> "OD2" Residue "L ASP 210": "OD1" <-> "OD2" Residue "L GLU 216": "OE1" <-> "OE2" Residue "L GLU 252": "OE1" <-> "OE2" Residue "L ASP 257": "OD1" <-> "OD2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L GLU 290": "OE1" <-> "OE2" Residue "L TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "M ASP 110": "OD1" <-> "OD2" Residue "M GLU 185": "OE1" <-> "OE2" Residue "M GLU 209": "OE1" <-> "OE2" Residue "N TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 38": "OD1" <-> "OD2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N ASP 91": "OD1" <-> "OD2" Residue "N GLU 172": "OE1" <-> "OE2" Residue "N PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 22": "OD1" <-> "OD2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 144": "OD1" <-> "OD2" Residue "O ASP 198": "OD1" <-> "OD2" Residue "O ASP 200": "OD1" <-> "OD2" Residue "O PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 85": "OD1" <-> "OD2" Residue "P TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 89": "OE1" <-> "OE2" Residue "P ASP 93": "OD1" <-> "OD2" Residue "P ASP 95": "OD1" <-> "OD2" Residue "P TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 157": "OD1" <-> "OD2" Residue "P GLU 180": "OE1" <-> "OE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "Q ASP 13": "OD1" <-> "OD2" Residue "Q PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 56": "OD1" <-> "OD2" Residue "Q ASP 64": "OD1" <-> "OD2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "Q PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "R ASP 115": "OD1" <-> "OD2" Residue "R PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ASP 102": "OD1" <-> "OD2" Residue "S ASP 111": "OD1" <-> "OD2" Residue "S GLU 172": "OE1" <-> "OE2" Residue "S GLU 174": "OE1" <-> "OE2" Residue "S GLU 179": "OE1" <-> "OE2" Residue "T ASP 7": "OD1" <-> "OD2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T ASP 101": "OD1" <-> "OD2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "T GLU 172": "OE1" <-> "OE2" Residue "T GLU 177": "OE1" <-> "OE2" Residue "U ASP 56": "OD1" <-> "OD2" Residue "U TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 114": "OE1" <-> "OE2" Residue "U PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 182": "OE1" <-> "OE2" Residue "U GLU 204": "OE1" <-> "OE2" Residue "U GLU 214": "OE1" <-> "OE2" Residue "U TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 34": "OD1" <-> "OD2" Residue "V TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 150": "OD1" <-> "OD2" Residue "V ASP 179": "OD1" <-> "OD2" Residue "V PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 218": "OE1" <-> "OE2" Residue "V ASP 219": "OD1" <-> "OD2" Residue "W ASP 82": "OD1" <-> "OD2" Residue "W GLU 84": "OE1" <-> "OE2" Residue "W TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 116": "OD1" <-> "OD2" Residue "W GLU 157": "OE1" <-> "OE2" Residue "W GLU 159": "OE1" <-> "OE2" Residue "W ASP 160": "OD1" <-> "OD2" Residue "W GLU 161": "OE1" <-> "OE2" Residue "W ASP 178": "OD1" <-> "OD2" Residue "W PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 193": "OE1" <-> "OE2" Residue "X ASP 11": "OD1" <-> "OD2" Residue "X ASP 18": "OD1" <-> "OD2" Residue "X GLU 31": "OE1" <-> "OE2" Residue "X PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 49": "OD1" <-> "OD2" Residue "X GLU 67": "OE1" <-> "OE2" Residue "X TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 184": "OE1" <-> "OE2" Residue "Y ASP 177": "OD1" <-> "OD2" Residue "Y ASP 198": "OD1" <-> "OD2" Residue "Y ASP 211": "OD1" <-> "OD2" Residue "Y GLU 216": "OE1" <-> "OE2" Residue "Y ASP 222": "OD1" <-> "OD2" Residue "Y ASP 224": "OD1" <-> "OD2" Residue "Z GLU 151": "OE1" <-> "OE2" Residue "Z TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 200": "OE1" <-> "OE2" Residue "Z ASP 210": "OD1" <-> "OD2" Residue "Z GLU 216": "OE1" <-> "OE2" Residue "Z GLU 246": "OE1" <-> "OE2" Residue "Z ASP 257": "OD1" <-> "OD2" Residue "Z GLU 268": "OE1" <-> "OE2" Residue "Z GLU 278": "OE1" <-> "OE2" Residue "Z GLU 290": "OE1" <-> "OE2" Residue "a ASP 24": "OD1" <-> "OD2" Residue "a GLU 65": "OE1" <-> "OE2" Residue "a GLU 98": "OE1" <-> "OE2" Residue "a GLU 127": "OE1" <-> "OE2" Residue "a GLU 153": "OE1" <-> "OE2" Residue "a GLU 156": "OE1" <-> "OE2" Residue "b ASP 53": "OD1" <-> "OD2" Residue "b ASP 60": "OD1" <-> "OD2" Residue "b GLU 93": "OE1" <-> "OE2" Residue "b GLU 169": "OE1" <-> "OE2" Residue "b GLU 172": "OE1" <-> "OE2" Residue "b ASP 185": "OD1" <-> "OD2" Residue "b GLU 200": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48318 Number of models: 1 Model: "" Number of chains: 30 Chain: "3" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 478 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain breaks: 2 Chain: "4" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 478 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 5, 'TRANS': 54} Chain breaks: 2 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1858 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain: "C" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1613 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1853 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "E" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "F" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1879 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} Chain: "G" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1843 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "H" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1659 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1594 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "J" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1542 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 3, 'TRANS': 189} Chain: "K" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1509 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "L" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1690 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "M" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1662 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain: "N" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1482 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain: "O" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1858 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain: "Q" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1613 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "R" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1853 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "S" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "T" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1879 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 4, 'TRANS': 229} Chain: "U" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1843 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 224} Chain: "V" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1659 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain: "W" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1594 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "X" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1542 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 3, 'TRANS': 189} Chain: "Y" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1509 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "Z" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1690 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "a" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1662 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain: "b" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1482 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 4, 'TRANS': 189} Time building chain proxies: 22.98, per 1000 atoms: 0.48 Number of scatterers: 48318 At special positions: 0 Unit cell: (181.308, 155.258, 128.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 246 16.00 O 9382 8.00 N 8052 7.00 C 30638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 108 " - pdb=" SG CYS G 152 " distance=2.04 Simple disulfide: pdb=" SG CYS U 108 " - pdb=" SG CYS U 152 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.82 Conformation dependent library (CDL) restraints added in 8.4 seconds 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11452 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 74 sheets defined 40.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain '3' and resid 81 through 86 Processing helix chain '3' and resid 102 through 106 Processing helix chain '4' and resid 81 through 86 Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.944A pdb=" N LEU A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 100 Processing helix chain 'A' and resid 104 through 122 removed outlier: 3.585A pdb=" N GLN A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.504A pdb=" N ARG A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 188 removed outlier: 4.828A pdb=" N SER A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.801A pdb=" N SER B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 91 Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.658A pdb=" N ILE B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 Processing helix chain 'B' and resid 173 through 189 Processing helix chain 'B' and resid 189 through 195 removed outlier: 4.509A pdb=" N ALA B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.819A pdb=" N LYS B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.504A pdb=" N SER C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 82 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 removed outlier: 3.899A pdb=" N PHE C 118 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 173 removed outlier: 3.840A pdb=" N VAL C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.749A pdb=" N THR C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.505A pdb=" N VAL D 61 " --> pdb=" O PRO D 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 62 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 101 removed outlier: 4.013A pdb=" N LYS D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 4.184A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 169 through 181 removed outlier: 4.341A pdb=" N GLN D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 200 removed outlier: 3.562A pdb=" N LYS D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 4.252A pdb=" N GLN D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 29 removed outlier: 3.915A pdb=" N ASN E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 109 through 122 Processing helix chain 'E' and resid 163 through 173 removed outlier: 4.266A pdb=" N CYS E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'F' and resid 16 through 27 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 78 through 99 removed outlier: 3.872A pdb=" N TYR F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER F 93 " --> pdb=" O ASN F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 121 removed outlier: 3.899A pdb=" N GLN F 117 " --> pdb=" O ASN F 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE F 118 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 119 " --> pdb=" O ILE F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 173 removed outlier: 3.933A pdb=" N THR F 169 " --> pdb=" O ARG F 165 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 170 " --> pdb=" O ILE F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 223 through 235 removed outlier: 4.176A pdb=" N TYR F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU F 229 " --> pdb=" O ASN F 225 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE F 230 " --> pdb=" O GLN F 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 17 through 29 Processing helix chain 'G' and resid 76 through 99 Processing helix chain 'G' and resid 103 through 121 Proline residue: G 117 - end of helix Processing helix chain 'G' and resid 163 through 175 Processing helix chain 'G' and resid 180 through 197 removed outlier: 3.775A pdb=" N SER G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 203 No H-bonds generated for 'chain 'G' and resid 201 through 203' Processing helix chain 'G' and resid 220 through 234 Processing helix chain 'H' and resid 54 through 77 Processing helix chain 'H' and resid 81 through 94 Processing helix chain 'H' and resid 95 through 97 No H-bonds generated for 'chain 'H' and resid 95 through 97' Processing helix chain 'H' and resid 136 through 148 removed outlier: 3.710A pdb=" N ILE H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 171 Processing helix chain 'H' and resid 209 through 213 removed outlier: 3.762A pdb=" N VAL H 213 " --> pdb=" O ARG H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.611A pdb=" N TYR I 8 " --> pdb=" O ILE I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 80 Processing helix chain 'I' and resid 84 through 98 Processing helix chain 'I' and resid 142 through 154 Processing helix chain 'I' and resid 159 through 176 Processing helix chain 'J' and resid 49 through 72 removed outlier: 3.586A pdb=" N ARG J 55 " --> pdb=" O GLY J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 93 removed outlier: 3.739A pdb=" N ASN J 91 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG J 93 " --> pdb=" O TYR J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 145 removed outlier: 3.550A pdb=" N PHE J 136 " --> pdb=" O ILE J 132 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR J 138 " --> pdb=" O THR J 134 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY J 139 " --> pdb=" O TYR J 135 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL J 140 " --> pdb=" O PHE J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 169 removed outlier: 3.567A pdb=" N LEU J 165 " --> pdb=" O CYS J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 102 Processing helix chain 'K' and resid 106 through 120 Processing helix chain 'K' and resid 162 through 172 removed outlier: 3.732A pdb=" N GLU K 172 " --> pdb=" O GLY K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 198 Processing helix chain 'K' and resid 224 through 226 No H-bonds generated for 'chain 'K' and resid 224 through 226' Processing helix chain 'L' and resid 145 through 164 Processing helix chain 'L' and resid 170 through 184 Processing helix chain 'L' and resid 226 through 238 Proline residue: L 232 - end of helix Processing helix chain 'L' and resid 251 through 270 Processing helix chain 'M' and resid 56 through 73 Processing helix chain 'M' and resid 78 through 96 Processing helix chain 'M' and resid 135 through 146 removed outlier: 4.338A pdb=" N LEU M 141 " --> pdb=" O ASN M 137 " (cutoff:3.500A) Proline residue: M 142 - end of helix removed outlier: 3.760A pdb=" N THR M 146 " --> pdb=" O PRO M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 152 removed outlier: 5.487A pdb=" N LEU M 150 " --> pdb=" O CYS M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 172 Processing helix chain 'M' and resid 202 through 206 removed outlier: 4.444A pdb=" N ASN M 206 " --> pdb=" O VAL M 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 92 removed outlier: 3.781A pdb=" N GLU N 82 " --> pdb=" O GLN N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 111 Processing helix chain 'N' and resid 147 through 152 Processing helix chain 'N' and resid 153 through 161 Processing helix chain 'N' and resid 166 through 183 Processing helix chain 'N' and resid 208 through 215 Processing helix chain 'O' and resid 18 through 30 removed outlier: 3.797A pdb=" N ASP O 22 " --> pdb=" O LEU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 100 Processing helix chain 'O' and resid 104 through 118 Processing helix chain 'O' and resid 119 through 121 No H-bonds generated for 'chain 'O' and resid 119 through 121' Processing helix chain 'O' and resid 164 through 171 removed outlier: 4.546A pdb=" N LEU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 185 Processing helix chain 'O' and resid 186 through 189 Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'O' and resid 213 through 225 removed outlier: 3.612A pdb=" N ILE O 224 " --> pdb=" O VAL O 220 " (cutoff:3.500A) Processing helix chain 'P' and resid 12 through 24 removed outlier: 3.597A pdb=" N SER P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS P 24 " --> pdb=" O LYS P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 91 Processing helix chain 'P' and resid 95 through 113 removed outlier: 3.644A pdb=" N ILE P 99 " --> pdb=" O ASP P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 167 removed outlier: 3.866A pdb=" N PHE P 167 " --> pdb=" O LEU P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 189 Processing helix chain 'P' and resid 190 through 194 Processing helix chain 'P' and resid 213 through 229 removed outlier: 3.758A pdb=" N ARG P 223 " --> pdb=" O ASN P 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE P 224 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN P 229 " --> pdb=" O GLU P 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 28 Processing helix chain 'Q' and resid 76 through 99 removed outlier: 3.504A pdb=" N SER Q 80 " --> pdb=" O ILE Q 76 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR Q 81 " --> pdb=" O LYS Q 77 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS Q 82 " --> pdb=" O PRO Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 120 removed outlier: 3.875A pdb=" N PHE Q 118 " --> pdb=" O TYR Q 114 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR Q 119 " --> pdb=" O LYS Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 171 removed outlier: 3.669A pdb=" N VAL Q 166 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 188 Processing helix chain 'Q' and resid 211 through 220 removed outlier: 3.852A pdb=" N VAL Q 215 " --> pdb=" O GLU Q 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 11 Processing helix chain 'R' and resid 19 through 30 removed outlier: 3.745A pdb=" N ASN R 29 " --> pdb=" O MET R 25 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU R 30 " --> pdb=" O GLN R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 62 removed outlier: 3.616A pdb=" N VAL R 61 " --> pdb=" O PRO R 58 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS R 62 " --> pdb=" O SER R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 101 removed outlier: 4.010A pdb=" N VAL R 82 " --> pdb=" O ILE R 78 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 118 removed outlier: 4.088A pdb=" N LEU R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 122 Processing helix chain 'R' and resid 169 through 181 removed outlier: 3.744A pdb=" N GLU R 178 " --> pdb=" O GLU R 174 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLN R 179 " --> pdb=" O ASN R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 200 Processing helix chain 'R' and resid 225 through 234 Processing helix chain 'S' and resid 19 through 29 removed outlier: 3.627A pdb=" N GLU S 23 " --> pdb=" O ILE S 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN S 26 " --> pdb=" O LEU S 22 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 99 Processing helix chain 'S' and resid 106 through 108 No H-bonds generated for 'chain 'S' and resid 106 through 108' Processing helix chain 'S' and resid 109 through 122 Processing helix chain 'S' and resid 163 through 173 removed outlier: 4.192A pdb=" N CYS S 167 " --> pdb=" O ARG S 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 181 removed outlier: 4.790A pdb=" N GLU S 179 " --> pdb=" O ASP S 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 198 Processing helix chain 'S' and resid 224 through 228 removed outlier: 4.052A pdb=" N GLU S 227 " --> pdb=" O LYS S 224 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 28 removed outlier: 3.533A pdb=" N ASN T 28 " --> pdb=" O LYS T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 59 Processing helix chain 'T' and resid 78 through 97 removed outlier: 3.831A pdb=" N TYR T 82 " --> pdb=" O THR T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 117 removed outlier: 3.782A pdb=" N GLN T 117 " --> pdb=" O ASN T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 120 No H-bonds generated for 'chain 'T' and resid 118 through 120' Processing helix chain 'T' and resid 163 through 173 removed outlier: 4.198A pdb=" N THR T 169 " --> pdb=" O ARG T 165 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU T 170 " --> pdb=" O ILE T 166 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 195 Processing helix chain 'T' and resid 214 through 216 No H-bonds generated for 'chain 'T' and resid 214 through 216' Processing helix chain 'T' and resid 223 through 235 removed outlier: 3.917A pdb=" N TYR T 227 " --> pdb=" O GLU T 223 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU T 229 " --> pdb=" O ASN T 225 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE T 230 " --> pdb=" O GLN T 226 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 7 Processing helix chain 'U' and resid 17 through 29 Processing helix chain 'U' and resid 76 through 99 Processing helix chain 'U' and resid 103 through 121 Proline residue: U 117 - end of helix Processing helix chain 'U' and resid 163 through 175 removed outlier: 3.697A pdb=" N LYS U 173 " --> pdb=" O LYS U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 197 removed outlier: 3.772A pdb=" N SER U 195 " --> pdb=" O GLY U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 201 through 203 No H-bonds generated for 'chain 'U' and resid 201 through 203' Processing helix chain 'U' and resid 220 through 234 Processing helix chain 'V' and resid 54 through 77 Processing helix chain 'V' and resid 81 through 94 Processing helix chain 'V' and resid 95 through 97 No H-bonds generated for 'chain 'V' and resid 95 through 97' Processing helix chain 'V' and resid 136 through 148 removed outlier: 3.681A pdb=" N ILE V 143 " --> pdb=" O ALA V 139 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 171 Processing helix chain 'V' and resid 209 through 213 removed outlier: 3.671A pdb=" N VAL V 213 " --> pdb=" O ARG V 210 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 9 removed outlier: 3.896A pdb=" N TYR W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 79 Processing helix chain 'W' and resid 84 through 98 Processing helix chain 'W' and resid 142 through 154 Processing helix chain 'W' and resid 159 through 177 removed outlier: 3.707A pdb=" N ARG W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 72 removed outlier: 3.545A pdb=" N ARG X 55 " --> pdb=" O GLY X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 93 removed outlier: 3.719A pdb=" N ASN X 91 " --> pdb=" O THR X 87 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG X 93 " --> pdb=" O TYR X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 145 removed outlier: 4.781A pdb=" N TYR X 138 " --> pdb=" O THR X 134 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY X 139 " --> pdb=" O TYR X 135 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL X 140 " --> pdb=" O PHE X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 169 Processing helix chain 'Y' and resid 79 through 102 Processing helix chain 'Y' and resid 106 through 120 Processing helix chain 'Y' and resid 162 through 174 removed outlier: 3.606A pdb=" N SER Y 173 " --> pdb=" O VAL Y 169 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 198 Processing helix chain 'Y' and resid 224 through 226 No H-bonds generated for 'chain 'Y' and resid 224 through 226' Processing helix chain 'Z' and resid 145 through 164 Processing helix chain 'Z' and resid 170 through 185 removed outlier: 3.769A pdb=" N LYS Z 185 " --> pdb=" O ILE Z 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 226 through 238 Proline residue: Z 232 - end of helix Processing helix chain 'Z' and resid 251 through 270 Processing helix chain 'a' and resid 56 through 73 Processing helix chain 'a' and resid 78 through 96 Processing helix chain 'a' and resid 135 through 145 removed outlier: 4.392A pdb=" N LEU a 141 " --> pdb=" O ASN a 137 " (cutoff:3.500A) Proline residue: a 142 - end of helix Processing helix chain 'a' and resid 146 through 147 No H-bonds generated for 'chain 'a' and resid 146 through 147' Processing helix chain 'a' and resid 148 through 152 Processing helix chain 'a' and resid 153 through 172 Processing helix chain 'a' and resid 201 through 205 removed outlier: 3.524A pdb=" N HIS a 205 " --> pdb=" O GLN a 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 69 through 91 removed outlier: 3.973A pdb=" N GLU b 82 " --> pdb=" O GLN b 78 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN b 85 " --> pdb=" O THR b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 111 removed outlier: 3.565A pdb=" N ILE b 107 " --> pdb=" O ALA b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 152 Processing helix chain 'b' and resid 153 through 161 Processing helix chain 'b' and resid 166 through 185 removed outlier: 3.572A pdb=" N ARG b 184 " --> pdb=" O CYS b 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 208 through 215 Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 157 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 67 removed outlier: 6.530A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 140 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 58 removed outlier: 6.602A pdb=" N VAL B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 135 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 146 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 64 removed outlier: 6.681A pdb=" N ILE C 69 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 152 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'D' and resid 163 through 166 Processing sheet with id=AA9, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.285A pdb=" N ILE D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 157 through 160 removed outlier: 3.604A pdb=" N ASP E 210 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE E 211 " --> pdb=" O ILE E 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 63 through 67 removed outlier: 6.759A pdb=" N SER E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU E 143 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 157 through 160 removed outlier: 3.538A pdb=" N ALA F 32 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 66 removed outlier: 6.350A pdb=" N ILE F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE F 143 " --> pdb=" O PHE F 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 157 through 160 Processing sheet with id=AB6, first strand: chain 'G' and resid 62 through 66 removed outlier: 6.236A pdb=" N PHE G 62 " --> pdb=" O PHE G 73 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N PHE G 73 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER G 71 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL G 143 " --> pdb=" O VAL G 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 130 through 132 removed outlier: 3.597A pdb=" N GLY H 17 " --> pdb=" O TYR H 14 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE H 178 " --> pdb=" O ASN H 193 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN H 193 " --> pdb=" O ILE H 178 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 25 through 28 removed outlier: 6.716A pdb=" N SER H 26 " --> pdb=" O ALA H 33 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 40 through 44 removed outlier: 3.524A pdb=" N ILE H 43 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE H 47 " --> pdb=" O ILE H 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 217 through 222 removed outlier: 3.568A pdb=" N LYS H 217 " --> pdb=" O GLU I 199 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP I 26 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N SER I 11 " --> pdb=" O ASP I 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 29 through 30 removed outlier: 3.537A pdb=" N SER I 37 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 43 through 47 removed outlier: 6.433A pdb=" N LEU I 50 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA I 121 " --> pdb=" O THR I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 127 through 130 Processing sheet with id=AC5, first strand: chain 'J' and resid 21 through 22 Processing sheet with id=AC6, first strand: chain 'J' and resid 35 through 38 Processing sheet with id=AC7, first strand: chain 'K' and resid 156 through 160 removed outlier: 3.574A pdb=" N GLY K 219 " --> pdb=" O LEU K 207 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE K 209 " --> pdb=" O HIS K 217 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N HIS K 217 " --> pdb=" O PHE K 209 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP K 211 " --> pdb=" O TRP K 215 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP K 215 " --> pdb=" O ASP K 211 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 65 through 69 removed outlier: 6.580A pdb=" N LEU K 72 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET K 131 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE K 142 " --> pdb=" O GLY K 154 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 220 through 223 Processing sheet with id=AD1, first strand: chain 'L' and resid 118 through 119 Processing sheet with id=AD2, first strand: chain 'L' and resid 132 through 135 removed outlier: 4.366A pdb=" N VAL L 206 " --> pdb=" O VAL L 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 32 through 35 removed outlier: 5.706A pdb=" N CYS M 33 " --> pdb=" O TYR M 29 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR M 29 " --> pdb=" O CYS M 33 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR M 48 " --> pdb=" O LEU M 44 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 32 through 35 removed outlier: 5.706A pdb=" N CYS M 33 " --> pdb=" O TYR M 29 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR M 29 " --> pdb=" O CYS M 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 130 through 133 removed outlier: 3.677A pdb=" N VAL M 10 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY M 18 " --> pdb=" O TYR M 15 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 130 through 133 removed outlier: 3.677A pdb=" N VAL M 10 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY M 18 " --> pdb=" O TYR M 15 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 209 through 211 Processing sheet with id=AD8, first strand: chain 'N' and resid 143 through 146 removed outlier: 3.507A pdb=" N GLY N 32 " --> pdb=" O TYR N 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET N 194 " --> pdb=" O PHE N 205 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N ILE a 210 " --> pdb=" O VAL N 202 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ARG N 204 " --> pdb=" O ILE a 210 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 41 through 43 removed outlier: 7.126A pdb=" N THR N 41 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 55 through 59 removed outlier: 6.337A pdb=" N ILE N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE N 129 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 154 through 157 removed outlier: 3.694A pdb=" N GLU O 208 " --> pdb=" O ARG O 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 63 through 65 Processing sheet with id=AE4, first strand: chain 'P' and resid 149 through 152 removed outlier: 4.531A pdb=" N ILE P 201 " --> pdb=" O LEU P 212 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG P 210 " --> pdb=" O TYR P 203 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 54 through 56 Processing sheet with id=AE6, first strand: chain 'P' and resid 146 through 147 removed outlier: 4.439A pdb=" N GLU P 146 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 156 through 159 Processing sheet with id=AE8, first strand: chain 'Q' and resid 61 through 64 removed outlier: 6.544A pdb=" N ILE Q 69 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER Q 152 " --> pdb=" O VAL Q 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 12 through 13 Processing sheet with id=AF1, first strand: chain 'R' and resid 163 through 166 removed outlier: 4.848A pdb=" N ILE R 213 " --> pdb=" O LEU R 224 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 65 through 68 removed outlier: 6.753A pdb=" N ILE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 157 through 160 removed outlier: 4.384A pdb=" N ILE S 211 " --> pdb=" O ILE S 223 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 63 through 67 removed outlier: 6.410A pdb=" N SER S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU S 143 " --> pdb=" O VAL S 155 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER S 151 " --> pdb=" O ASP S 147 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 157 through 160 Processing sheet with id=AF6, first strand: chain 'T' and resid 63 through 64 removed outlier: 3.811A pdb=" N ILE T 143 " --> pdb=" O PHE T 155 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 157 through 160 Processing sheet with id=AF8, first strand: chain 'U' and resid 62 through 66 removed outlier: 6.769A pdb=" N LEU U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL U 143 " --> pdb=" O VAL U 155 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 130 through 133 removed outlier: 3.517A pdb=" N GLY V 17 " --> pdb=" O TYR V 14 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE V 178 " --> pdb=" O ASN V 193 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN V 193 " --> pdb=" O ILE V 178 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 26 through 28 removed outlier: 6.568A pdb=" N SER V 26 " --> pdb=" O ALA V 33 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE V 31 " --> pdb=" O SER V 28 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 41 through 44 removed outlier: 6.231A pdb=" N ILE V 47 " --> pdb=" O ILE V 43 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 217 through 222 removed outlier: 3.519A pdb=" N LYS V 217 " --> pdb=" O GLU W 199 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER W 11 " --> pdb=" O ASP W 26 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 29 through 30 Processing sheet with id=AG5, first strand: chain 'W' and resid 43 through 47 removed outlier: 6.437A pdb=" N LEU W 50 " --> pdb=" O LEU W 46 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA W 121 " --> pdb=" O THR W 133 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 127 through 130 removed outlier: 3.712A pdb=" N PHE X 12 " --> pdb=" O GLY X 9 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 21 through 22 Processing sheet with id=AG8, first strand: chain 'X' and resid 35 through 39 removed outlier: 6.245A pdb=" N PHE X 35 " --> pdb=" O TYR X 46 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR X 46 " --> pdb=" O PHE X 35 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASN X 37 " --> pdb=" O PHE X 44 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE X 44 " --> pdb=" O ASN X 37 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN X 39 " --> pdb=" O VAL X 42 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 156 through 160 removed outlier: 3.611A pdb=" N GLY Y 219 " --> pdb=" O LEU Y 207 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE Y 209 " --> pdb=" O HIS Y 217 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS Y 217 " --> pdb=" O PHE Y 209 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP Y 211 " --> pdb=" O TRP Y 215 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP Y 215 " --> pdb=" O ASP Y 211 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 51 through 53 removed outlier: 7.094A pdb=" N ALA Y 51 " --> pdb=" O ALA Y 58 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 65 through 69 removed outlier: 6.571A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 68 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET Y 131 " --> pdb=" O THR Y 75 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS Y 139 " --> pdb=" O ASP Y 136 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE Y 142 " --> pdb=" O GLY Y 154 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 220 through 223 Processing sheet with id=AH4, first strand: chain 'Z' and resid 118 through 120 removed outlier: 5.669A pdb=" N SER Z 120 " --> pdb=" O ILE Z 124 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE Z 124 " --> pdb=" O SER Z 120 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 132 through 135 removed outlier: 4.347A pdb=" N VAL Z 206 " --> pdb=" O VAL Z 218 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'a' and resid 32 through 35 removed outlier: 5.650A pdb=" N CYS a 33 " --> pdb=" O TYR a 29 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR a 29 " --> pdb=" O CYS a 33 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR a 48 " --> pdb=" O LEU a 44 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'a' and resid 32 through 35 removed outlier: 5.650A pdb=" N CYS a 33 " --> pdb=" O TYR a 29 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR a 29 " --> pdb=" O CYS a 33 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 130 through 132 removed outlier: 3.626A pdb=" N GLY a 18 " --> pdb=" O TYR a 15 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'a' and resid 130 through 132 removed outlier: 3.626A pdb=" N GLY a 18 " --> pdb=" O TYR a 15 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'b' and resid 41 through 43 removed outlier: 6.035A pdb=" N MET b 43 " --> pdb=" O VAL b 47 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL b 47 " --> pdb=" O MET b 43 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'b' and resid 55 through 59 removed outlier: 6.312A pdb=" N ILE b 62 " --> pdb=" O ILE b 58 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE b 129 " --> pdb=" O ALA b 141 " (cutoff:3.500A) 2786 hydrogen bonds defined for protein. 7911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.71 Time building geometry restraints manager: 20.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 15787 1.35 - 1.47: 11320 1.47 - 1.59: 21659 1.59 - 1.71: 0 1.71 - 1.83: 374 Bond restraints: 49140 Sorted by residual: bond pdb=" N SER G 2 " pdb=" CA SER G 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N ALA C 6 " pdb=" CA ALA C 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N ALA F 2 " pdb=" CA ALA F 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N ALA Q 6 " pdb=" CA ALA Q 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LYS Z 90 " pdb=" CA LYS Z 90 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 49135 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.14: 712 106.14 - 113.12: 26398 113.12 - 120.09: 17285 120.09 - 127.06: 21590 127.06 - 134.03: 269 Bond angle restraints: 66254 Sorted by residual: angle pdb=" N VAL K 68 " pdb=" CA VAL K 68 " pdb=" C VAL K 68 " ideal model delta sigma weight residual 112.96 109.13 3.83 1.00e+00 1.00e+00 1.47e+01 angle pdb=" N THR Y 220 " pdb=" CA THR Y 220 " pdb=" C THR Y 220 " ideal model delta sigma weight residual 110.44 106.24 4.20 1.20e+00 6.94e-01 1.22e+01 angle pdb=" CA ARG R 17 " pdb=" CB ARG R 17 " pdb=" CG ARG R 17 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N VAL R 61 " pdb=" CA VAL R 61 " pdb=" C VAL R 61 " ideal model delta sigma weight residual 111.91 109.04 2.87 8.90e-01 1.26e+00 1.04e+01 angle pdb=" N SER W 31 " pdb=" CA SER W 31 " pdb=" C SER W 31 " ideal model delta sigma weight residual 110.88 106.82 4.06 1.28e+00 6.10e-01 1.01e+01 ... (remaining 66249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 26533 17.96 - 35.91: 2425 35.91 - 53.87: 559 53.87 - 71.82: 126 71.82 - 89.78: 63 Dihedral angle restraints: 29706 sinusoidal: 11802 harmonic: 17904 Sorted by residual: dihedral pdb=" CB CYS G 108 " pdb=" SG CYS G 108 " pdb=" SG CYS G 152 " pdb=" CB CYS G 152 " ideal model delta sinusoidal sigma weight residual 93.00 148.26 -55.26 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS U 108 " pdb=" SG CYS U 108 " pdb=" SG CYS U 152 " pdb=" CB CYS U 152 " ideal model delta sinusoidal sigma weight residual 93.00 147.18 -54.18 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CA THR L 273 " pdb=" C THR L 273 " pdb=" N GLY L 274 " pdb=" CA GLY L 274 " ideal model delta harmonic sigma weight residual 180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 29703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4782 0.031 - 0.062: 1693 0.062 - 0.093: 455 0.093 - 0.125: 431 0.125 - 0.156: 39 Chirality restraints: 7400 Sorted by residual: chirality pdb=" CA ILE V 9 " pdb=" N ILE V 9 " pdb=" C ILE V 9 " pdb=" CB ILE V 9 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CA ILE b 119 " pdb=" N ILE b 119 " pdb=" C ILE b 119 " pdb=" CB ILE b 119 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE C 9 " pdb=" N ILE C 9 " pdb=" C ILE C 9 " pdb=" CB ILE C 9 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 7397 not shown) Planarity restraints: 8522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG b 199 " 0.218 9.50e-02 1.11e+02 9.80e-02 6.82e+00 pdb=" NE ARG b 199 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG b 199 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG b 199 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG b 199 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 199 " -0.213 9.50e-02 1.11e+02 9.58e-02 6.26e+00 pdb=" NE ARG N 199 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG N 199 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG N 199 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG N 199 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 225 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO D 226 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 226 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 226 " -0.025 5.00e-02 4.00e+02 ... (remaining 8519 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 119 2.43 - 3.05: 31768 3.05 - 3.66: 73505 3.66 - 4.28: 118120 4.28 - 4.90: 200925 Nonbonded interactions: 424437 Sorted by model distance: nonbonded pdb=" OG SER F 103 " pdb=" OD1 ASP N 91 " model vdw 1.810 2.440 nonbonded pdb=" OD1 ASP Z 96 " pdb=" OG SER Z 98 " model vdw 1.943 2.440 nonbonded pdb=" OG1 THR W 114 " pdb=" OD1 ASP W 116 " model vdw 2.041 2.440 nonbonded pdb=" OE1 GLU O 110 " pdb=" OH TYR O 149 " model vdw 2.042 2.440 nonbonded pdb=" N GLU H 186 " pdb=" OE1 GLU H 186 " model vdw 2.091 2.520 ... (remaining 424432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '3' selection = chain '4' } ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.240 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: 0.040 Extract box with map and model: 16.140 Check model and map are aligned: 0.660 Set scattering table: 0.430 Process input model: 122.540 Find NCS groups from input model: 4.800 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.003 0.039 49140 Z= 0.204 Angle : 0.542 7.096 66254 Z= 0.318 Chirality : 0.042 0.156 7400 Planarity : 0.003 0.098 8522 Dihedral : 15.313 89.781 18248 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.85 % Allowed : 13.68 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.11), residues: 6092 helix: 1.43 (0.11), residues: 2150 sheet: 0.39 (0.13), residues: 1430 loop : -0.29 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 280 HIS 0.005 0.001 HIS G 92 PHE 0.029 0.001 PHE K 221 TYR 0.019 0.001 TYR G 66 ARG 0.017 0.000 ARG b 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 722 time to evaluate : 6.138 Fit side-chains revert: symmetry clash REVERT: 3 141 ASP cc_start: 0.5517 (p0) cc_final: 0.4930 (t0) REVERT: 4 140 ASP cc_start: 0.5894 (t0) cc_final: 0.5673 (p0) REVERT: 4 143 ASN cc_start: 0.7738 (m-40) cc_final: 0.7522 (m-40) REVERT: A 80 ASP cc_start: 0.9025 (m-30) cc_final: 0.8671 (m-30) REVERT: A 142 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7426 (ttp-170) REVERT: B 176 ARG cc_start: 0.7554 (ttt180) cc_final: 0.7330 (ttt-90) REVERT: C 86 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7902 (tp30) REVERT: C 153 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7217 (tm-30) REVERT: C 198 MET cc_start: 0.6505 (mpp) cc_final: 0.6260 (mpp) REVERT: D 3 ILE cc_start: 0.7991 (mt) cc_final: 0.7584 (pt) REVERT: D 203 LYS cc_start: 0.6719 (mttt) cc_final: 0.6109 (tttm) REVERT: E 147 ASP cc_start: 0.7417 (m-30) cc_final: 0.7185 (p0) REVERT: E 163 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7428 (mtp85) REVERT: F 70 PHE cc_start: 0.7967 (p90) cc_final: 0.7276 (p90) REVERT: G 66 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8981 (t80) REVERT: H 9 ILE cc_start: 0.8618 (pp) cc_final: 0.8349 (pp) REVERT: H 97 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8280 (mm110) REVERT: H 161 CYS cc_start: 0.8266 (m) cc_final: 0.8060 (t) REVERT: H 185 GLN cc_start: 0.7496 (tp40) cc_final: 0.7283 (mm110) REVERT: I 195 TYR cc_start: 0.9294 (p90) cc_final: 0.8661 (p90) REVERT: L 257 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7277 (t0) REVERT: M 138 MET cc_start: 0.8101 (mtm) cc_final: 0.7898 (mtp) REVERT: O 144 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.6485 (m-30) REVERT: O 207 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7599 (mp10) REVERT: P 11 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7445 (mtp85) REVERT: P 19 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8041 (mm) REVERT: P 73 MET cc_start: 0.8152 (mmp) cc_final: 0.7913 (mmm) REVERT: Q 24 GLN cc_start: 0.7430 (tt0) cc_final: 0.7015 (tt0) REVERT: Q 64 ASP cc_start: 0.7307 (t0) cc_final: 0.6443 (t0) REVERT: Q 86 GLU cc_start: 0.8220 (tp30) cc_final: 0.7983 (tp30) REVERT: Q 105 ASP cc_start: 0.7935 (t0) cc_final: 0.7711 (t70) REVERT: R 111 GLU cc_start: 0.7925 (tt0) cc_final: 0.7632 (tt0) REVERT: R 231 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8189 (tt0) REVERT: S 10 TYR cc_start: 0.8846 (p90) cc_final: 0.8484 (p90) REVERT: S 30 GLN cc_start: 0.7607 (mt0) cc_final: 0.7406 (mt0) REVERT: S 43 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6156 (p90) REVERT: T 100 MET cc_start: 0.8689 (mtt) cc_final: 0.8353 (mtm) REVERT: U 186 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8105 (mp0) REVERT: V 97 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8273 (mm110) REVERT: V 186 GLU cc_start: 0.7576 (mp0) cc_final: 0.7131 (mp0) REVERT: V 190 MET cc_start: 0.8082 (ttt) cc_final: 0.7721 (mtm) REVERT: W 80 ASN cc_start: 0.6903 (OUTLIER) cc_final: 0.6518 (m-40) REVERT: W 144 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8045 (tttm) REVERT: W 195 TYR cc_start: 0.9330 (p90) cc_final: 0.8694 (p90) REVERT: Y 175 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7987 (mtp-110) REVERT: a 1 MET cc_start: 0.8269 (ttt) cc_final: 0.7855 (ttp) REVERT: a 98 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6369 (tm-30) outliers start: 45 outliers final: 29 residues processed: 754 average time/residue: 1.6171 time to fit residues: 1513.4541 Evaluate side-chains 695 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 660 time to evaluate : 5.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain O residue 144 ASP Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 137 ASP Chi-restraints excluded: chain V residue 77 ASN Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain Y residue 101 ASN Chi-restraints excluded: chain a residue 181 ILE Chi-restraints excluded: chain a residue 201 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 0.7980 chunk 456 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 307 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 471 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 286 optimal weight: 0.0070 chunk 351 optimal weight: 0.0030 chunk 546 optimal weight: 5.9990 overall best weight: 1.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 112 GLN B 206 ASN C 150 ASN D 64 HIS E 27 ASN F 86 ASN G 59 GLN H 92 HIS I 79 ASN I 191 ASN J 39 ASN K 124 GLN K 150 GLN K 204 ASN P 112 GLN Q 39 ASN Q 116 GLN Q 150 ASN S 107 HIS U 92 HIS U 120 GLN U 203 GLN V 77 ASN W 79 ASN Y 124 GLN Y 196 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 49140 Z= 0.263 Angle : 0.571 19.382 66254 Z= 0.310 Chirality : 0.045 0.190 7400 Planarity : 0.004 0.051 8522 Dihedral : 6.024 121.361 6751 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.89 % Allowed : 13.74 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.11), residues: 6092 helix: 1.69 (0.11), residues: 2192 sheet: 0.60 (0.13), residues: 1340 loop : -0.30 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Z 280 HIS 0.007 0.001 HIS U 92 PHE 0.020 0.002 PHE A 81 TYR 0.018 0.001 TYR L 193 ARG 0.006 0.000 ARG N 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 720 time to evaluate : 5.452 Fit side-chains REVERT: 3 135 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8068 (ttmt) REVERT: 3 141 ASP cc_start: 0.5404 (OUTLIER) cc_final: 0.4832 (t0) REVERT: 4 135 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8086 (ttmt) REVERT: 4 143 ASN cc_start: 0.7723 (m-40) cc_final: 0.7472 (m-40) REVERT: A 149 TYR cc_start: 0.8840 (p90) cc_final: 0.8496 (p90) REVERT: B 8 GLU cc_start: 0.8190 (tp30) cc_final: 0.7978 (tp30) REVERT: B 176 ARG cc_start: 0.7529 (ttt180) cc_final: 0.7290 (ttt-90) REVERT: C 24 GLN cc_start: 0.7410 (tt0) cc_final: 0.7152 (tt0) REVERT: C 79 ASP cc_start: 0.8927 (m-30) cc_final: 0.8386 (m-30) REVERT: C 153 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7175 (tm-30) REVERT: C 198 MET cc_start: 0.6591 (mpp) cc_final: 0.6369 (mpp) REVERT: D 17 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6867 (mtm110) REVERT: D 203 LYS cc_start: 0.6709 (mttt) cc_final: 0.6073 (tttm) REVERT: E 43 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6115 (p90) REVERT: E 226 GLU cc_start: 0.8308 (mp0) cc_final: 0.8019 (mp0) REVERT: F 70 PHE cc_start: 0.8097 (p90) cc_final: 0.7456 (p90) REVERT: F 179 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7774 (ttm) REVERT: F 211 MET cc_start: 0.8559 (ttm) cc_final: 0.8339 (ttm) REVERT: H 97 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8257 (mm110) REVERT: H 151 MET cc_start: 0.8923 (mtm) cc_final: 0.8638 (mtm) REVERT: H 185 GLN cc_start: 0.7498 (tp40) cc_final: 0.7279 (mm110) REVERT: I 116 ASP cc_start: 0.7626 (t0) cc_final: 0.7394 (t0) REVERT: I 183 MET cc_start: 0.6294 (ptt) cc_final: 0.6075 (ttp) REVERT: I 189 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8707 (tp) REVERT: I 195 TYR cc_start: 0.9296 (p90) cc_final: 0.8610 (p90) REVERT: K 98 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8326 (tm-30) REVERT: K 175 ARG cc_start: 0.8433 (mtm110) cc_final: 0.8123 (mtp-110) REVERT: L 161 GLN cc_start: 0.8163 (pp30) cc_final: 0.7926 (mp10) REVERT: L 164 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: M 148 ASN cc_start: 0.7629 (p0) cc_final: 0.7245 (p0) REVERT: N 86 ARG cc_start: 0.7771 (ttt90) cc_final: 0.7512 (tpt-90) REVERT: N 106 ASP cc_start: 0.7740 (m-30) cc_final: 0.7422 (m-30) REVERT: N 140 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: N 142 GLU cc_start: 0.8053 (tp30) cc_final: 0.7748 (pm20) REVERT: N 193 ARG cc_start: 0.8268 (mtt-85) cc_final: 0.7945 (mtp85) REVERT: O 149 TYR cc_start: 0.8830 (p90) cc_final: 0.8401 (p90) REVERT: O 207 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7533 (mp10) REVERT: P 11 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7376 (mtp85) REVERT: P 73 MET cc_start: 0.8266 (mmp) cc_final: 0.8057 (mmm) REVERT: Q 24 GLN cc_start: 0.7523 (tt0) cc_final: 0.7099 (tt0) REVERT: Q 64 ASP cc_start: 0.7416 (t0) cc_final: 0.6825 (t0) REVERT: Q 66 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6580 (p0) REVERT: Q 94 TYR cc_start: 0.8963 (t80) cc_final: 0.8756 (t80) REVERT: Q 143 TYR cc_start: 0.8682 (m-80) cc_final: 0.8228 (m-80) REVERT: Q 148 ASP cc_start: 0.7941 (p0) cc_final: 0.7720 (p0) REVERT: Q 153 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: R 111 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: S 30 GLN cc_start: 0.7570 (mt0) cc_final: 0.7358 (mt0) REVERT: S 43 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.5960 (p90) REVERT: S 163 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7789 (mtt90) REVERT: T 100 MET cc_start: 0.8747 (mtt) cc_final: 0.8339 (mtm) REVERT: U 50 GLN cc_start: 0.6078 (OUTLIER) cc_final: 0.5841 (pt0) REVERT: U 177 GLU cc_start: 0.6780 (mp0) cc_final: 0.6461 (mt-10) REVERT: U 186 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: U 225 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7713 (tm-30) REVERT: V 97 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8263 (mm110) REVERT: V 186 GLU cc_start: 0.7601 (mp0) cc_final: 0.7180 (mp0) REVERT: V 190 MET cc_start: 0.8023 (ttt) cc_final: 0.7792 (mtm) REVERT: W 80 ASN cc_start: 0.6695 (OUTLIER) cc_final: 0.6265 (m-40) REVERT: W 132 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: W 144 LYS cc_start: 0.8410 (ttmt) cc_final: 0.7994 (tttm) REVERT: W 195 TYR cc_start: 0.9314 (p90) cc_final: 0.8693 (p90) REVERT: Y 175 ARG cc_start: 0.8417 (mtm110) cc_final: 0.8114 (mtp-110) REVERT: Y 213 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7984 (m-40) REVERT: Z 164 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: Z 246 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6216 (tt0) REVERT: a 1 MET cc_start: 0.8180 (ttt) cc_final: 0.7813 (ttp) REVERT: a 98 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6407 (tm-30) REVERT: a 202 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6179 (pm20) REVERT: b 106 ASP cc_start: 0.7717 (m-30) cc_final: 0.7454 (m-30) REVERT: b 140 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7637 (tp30) outliers start: 153 outliers final: 51 residues processed: 792 average time/residue: 1.5438 time to fit residues: 1531.6971 Evaluate side-chains 726 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 652 time to evaluate : 7.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 153 GLU Chi-restraints excluded: chain Q residue 198 MET Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 50 GLN Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 213 ASN Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 454 optimal weight: 0.9990 chunk 372 optimal weight: 9.9990 chunk 150 optimal weight: 0.0050 chunk 547 optimal weight: 3.9990 chunk 591 optimal weight: 3.9990 chunk 487 optimal weight: 0.7980 chunk 543 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 439 optimal weight: 3.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 107 HIS G 59 GLN G 120 GLN K 124 GLN K 204 ASN M 17 ASN N 203 GLN ** P 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN Q 39 ASN Q 116 GLN Q 150 ASN U 92 HIS U 120 GLN U 203 GLN V 77 ASN V 122 HIS V 177 ASN W 79 ASN Y 124 GLN a 70 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 49140 Z= 0.228 Angle : 0.535 20.835 66254 Z= 0.289 Chirality : 0.044 0.185 7400 Planarity : 0.004 0.052 8522 Dihedral : 5.632 113.969 6722 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.11 % Allowed : 14.72 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.11), residues: 6092 helix: 1.82 (0.11), residues: 2200 sheet: 0.63 (0.13), residues: 1358 loop : -0.31 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 280 HIS 0.006 0.001 HIS U 92 PHE 0.028 0.002 PHE P 214 TYR 0.016 0.001 TYR Z 193 ARG 0.012 0.000 ARG E 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 712 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8064 (ttmt) REVERT: 3 141 ASP cc_start: 0.5499 (OUTLIER) cc_final: 0.4894 (t0) REVERT: 4 135 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7976 (ttmt) REVERT: A 64 TYR cc_start: 0.8439 (m-80) cc_final: 0.8035 (m-80) REVERT: A 149 TYR cc_start: 0.8804 (p90) cc_final: 0.8429 (p90) REVERT: B 8 GLU cc_start: 0.7919 (tp30) cc_final: 0.7629 (tp30) REVERT: B 73 MET cc_start: 0.8405 (mmm) cc_final: 0.8090 (mmp) REVERT: C 24 GLN cc_start: 0.7447 (tt0) cc_final: 0.7202 (tt0) REVERT: C 40 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: C 153 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7067 (tm-30) REVERT: D 17 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6901 (mtm110) REVERT: D 176 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7323 (ttp) REVERT: D 203 LYS cc_start: 0.6690 (mttt) cc_final: 0.6058 (tttm) REVERT: E 43 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.6094 (p90) REVERT: E 49 TYR cc_start: 0.7731 (t80) cc_final: 0.7453 (t80) REVERT: F 179 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7867 (ttm) REVERT: H 97 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8245 (mm110) REVERT: H 151 MET cc_start: 0.8911 (mtm) cc_final: 0.8662 (mtm) REVERT: H 185 GLN cc_start: 0.7483 (tp40) cc_final: 0.7259 (mm110) REVERT: I 116 ASP cc_start: 0.7582 (t70) cc_final: 0.7258 (t0) REVERT: I 183 MET cc_start: 0.6481 (ptt) cc_final: 0.6248 (ttp) REVERT: I 195 TYR cc_start: 0.9288 (p90) cc_final: 0.8668 (p90) REVERT: K 76 MET cc_start: 0.7862 (ptm) cc_final: 0.7641 (ptm) REVERT: K 98 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8405 (tm-30) REVERT: K 175 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8142 (mtp-110) REVERT: L 161 GLN cc_start: 0.8215 (pp30) cc_final: 0.7989 (mp10) REVERT: L 164 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7259 (tp30) REVERT: L 202 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7387 (t0) REVERT: L 268 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: L 290 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7810 (mm-30) REVERT: M 148 ASN cc_start: 0.7686 (p0) cc_final: 0.7318 (p0) REVERT: N 86 ARG cc_start: 0.7727 (ttt90) cc_final: 0.7316 (tpt-90) REVERT: N 102 MET cc_start: 0.8489 (mmt) cc_final: 0.8189 (mmt) REVERT: N 106 ASP cc_start: 0.7767 (m-30) cc_final: 0.7459 (m-30) REVERT: N 142 GLU cc_start: 0.8039 (tp30) cc_final: 0.7746 (pm20) REVERT: N 193 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.7980 (mtp85) REVERT: O 149 TYR cc_start: 0.8854 (p90) cc_final: 0.8337 (p90) REVERT: O 159 ARG cc_start: 0.6856 (pmt-80) cc_final: 0.6569 (ppt170) REVERT: P 11 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7342 (mtp85) REVERT: Q 24 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7053 (tt0) REVERT: Q 64 ASP cc_start: 0.7366 (t0) cc_final: 0.6812 (t0) REVERT: Q 66 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6496 (p0) REVERT: Q 143 TYR cc_start: 0.8600 (m-80) cc_final: 0.8387 (m-80) REVERT: Q 153 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: R 17 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6586 (mpt180) REVERT: R 97 GLU cc_start: 0.8479 (tt0) cc_final: 0.8196 (tt0) REVERT: R 111 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: S 30 GLN cc_start: 0.7577 (mt0) cc_final: 0.7359 (mt0) REVERT: S 43 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.5961 (p90) REVERT: T 100 MET cc_start: 0.8735 (mtt) cc_final: 0.8382 (mtm) REVERT: U 50 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5881 (pt0) REVERT: U 186 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: V 97 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8252 (mm110) REVERT: V 154 GLU cc_start: 0.7702 (pt0) cc_final: 0.6899 (tp30) REVERT: W 132 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: W 144 LYS cc_start: 0.8411 (ttmt) cc_final: 0.8004 (tttm) REVERT: W 195 TYR cc_start: 0.9324 (p90) cc_final: 0.8682 (p90) REVERT: X 95 HIS cc_start: 0.7110 (m90) cc_final: 0.6507 (m-70) REVERT: X 124 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: Y 98 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8346 (tm-30) REVERT: Y 175 ARG cc_start: 0.8384 (mtm110) cc_final: 0.8098 (mtp-110) REVERT: Y 213 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.8022 (m-40) REVERT: Z 164 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: Z 246 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6203 (tt0) REVERT: a 1 MET cc_start: 0.8178 (ttt) cc_final: 0.7854 (ttp) REVERT: a 98 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6318 (tm-30) REVERT: a 202 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.6021 (pm20) REVERT: b 86 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7122 (tpt-90) REVERT: b 106 ASP cc_start: 0.7826 (m-30) cc_final: 0.7574 (m-30) REVERT: b 114 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8630 (mtm) REVERT: b 140 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: b 142 GLU cc_start: 0.7957 (tp30) cc_final: 0.7743 (pm20) outliers start: 165 outliers final: 58 residues processed: 799 average time/residue: 1.5520 time to fit residues: 1549.9006 Evaluate side-chains 765 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 679 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 202 ASP Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 153 GLU Chi-restraints excluded: chain R residue 17 ARG Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain T residue 229 GLU Chi-restraints excluded: chain U residue 50 GLN Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain U residue 231 ILE Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 213 ASN Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 201 TRP Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 MET Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 4.9990 chunk 411 optimal weight: 6.9990 chunk 284 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 367 optimal weight: 5.9990 chunk 549 optimal weight: 2.9990 chunk 581 optimal weight: 0.8980 chunk 287 optimal weight: 8.9990 chunk 520 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 112 GLN B 114 ASN G 52 HIS G 59 GLN G 120 GLN H 77 ASN I 79 ASN K 124 GLN K 150 GLN K 204 ASN N 203 GLN ** P 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN Q 39 ASN R 26 GLN ** S 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 HIS U 120 GLN U 203 GLN V 77 ASN W 79 ASN W 80 ASN Y 124 GLN Y 150 GLN Y 206 ASN a 206 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 49140 Z= 0.341 Angle : 0.582 23.427 66254 Z= 0.311 Chirality : 0.046 0.199 7400 Planarity : 0.004 0.052 8522 Dihedral : 5.701 103.556 6715 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.85 % Allowed : 15.53 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.11), residues: 6092 helix: 1.68 (0.11), residues: 2196 sheet: 0.54 (0.13), residues: 1358 loop : -0.39 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 280 HIS 0.008 0.001 HIS G 92 PHE 0.036 0.002 PHE P 214 TYR 0.019 0.002 TYR Z 193 ARG 0.010 0.001 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 692 time to evaluate : 5.712 Fit side-chains revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8077 (ttmt) REVERT: 3 141 ASP cc_start: 0.5431 (OUTLIER) cc_final: 0.4896 (t0) REVERT: 4 83 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6382 (m-30) REVERT: 4 135 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8097 (ttmt) REVERT: A 61 LYS cc_start: 0.7687 (mttm) cc_final: 0.7411 (mtmt) REVERT: A 149 TYR cc_start: 0.8832 (p90) cc_final: 0.8451 (p90) REVERT: B 8 GLU cc_start: 0.7918 (tp30) cc_final: 0.7614 (tp30) REVERT: B 73 MET cc_start: 0.8468 (mmm) cc_final: 0.8150 (mmp) REVERT: B 174 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7370 (mtp) REVERT: B 184 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7406 (tp) REVERT: C 13 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6760 (p0) REVERT: C 37 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7458 (t0) REVERT: C 40 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6725 (pm20) REVERT: C 153 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7032 (tm-30) REVERT: D 17 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6931 (mtm110) REVERT: D 176 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7351 (mtm) REVERT: D 203 LYS cc_start: 0.6771 (mttt) cc_final: 0.6128 (tttm) REVERT: E 6 ASP cc_start: 0.7213 (m-30) cc_final: 0.6913 (m-30) REVERT: E 43 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.6006 (p90) REVERT: E 183 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7861 (ttpt) REVERT: F 70 PHE cc_start: 0.8230 (p90) cc_final: 0.7332 (p90) REVERT: H 97 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8237 (mm110) REVERT: H 151 MET cc_start: 0.8886 (mtm) cc_final: 0.8643 (mtm) REVERT: H 185 GLN cc_start: 0.7483 (tp40) cc_final: 0.7254 (mm110) REVERT: I 116 ASP cc_start: 0.7590 (t70) cc_final: 0.7231 (t0) REVERT: I 195 TYR cc_start: 0.9327 (p90) cc_final: 0.8689 (p90) REVERT: J 124 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: J 183 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8167 (ptmm) REVERT: K 98 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8391 (tm-30) REVERT: L 137 ASP cc_start: 0.7667 (m-30) cc_final: 0.7403 (m-30) REVERT: L 161 GLN cc_start: 0.8189 (pp30) cc_final: 0.7926 (mp10) REVERT: L 164 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: L 202 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7554 (t0) REVERT: L 268 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: M 148 ASN cc_start: 0.7756 (p0) cc_final: 0.7393 (p0) REVERT: N 91 ASP cc_start: 0.8459 (m-30) cc_final: 0.8210 (t0) REVERT: N 102 MET cc_start: 0.8433 (mmt) cc_final: 0.8194 (mmt) REVERT: N 106 ASP cc_start: 0.7743 (m-30) cc_final: 0.7412 (m-30) REVERT: N 140 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: N 193 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.8032 (mtp85) REVERT: O 149 TYR cc_start: 0.8862 (p90) cc_final: 0.8449 (p90) REVERT: O 207 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7551 (mp10) REVERT: P 11 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7403 (mtp85) REVERT: Q 24 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: Q 64 ASP cc_start: 0.7361 (t0) cc_final: 0.7104 (t0) REVERT: Q 66 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6820 (p0) REVERT: Q 143 TYR cc_start: 0.8650 (m-80) cc_final: 0.8257 (m-80) REVERT: Q 153 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: R 97 GLU cc_start: 0.8489 (tt0) cc_final: 0.8181 (tt0) REVERT: R 111 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: R 174 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7546 (mm-30) REVERT: S 30 GLN cc_start: 0.7720 (mt0) cc_final: 0.7447 (mt0) REVERT: S 38 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8259 (mp) REVERT: S 43 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.5872 (p90) REVERT: S 163 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7783 (mtt90) REVERT: S 206 LYS cc_start: 0.7947 (pttt) cc_final: 0.7618 (mtpt) REVERT: T 50 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7057 (mm-30) REVERT: T 100 MET cc_start: 0.8731 (mtt) cc_final: 0.8294 (mtm) REVERT: U 145 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7926 (ppp) REVERT: U 186 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: V 97 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8263 (mm110) REVERT: V 151 MET cc_start: 0.8814 (mtm) cc_final: 0.8566 (mtm) REVERT: V 154 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: W 80 ASN cc_start: 0.6800 (OUTLIER) cc_final: 0.6443 (m-40) REVERT: W 195 TYR cc_start: 0.9347 (p90) cc_final: 0.8665 (p90) REVERT: W 198 ARG cc_start: 0.8727 (mtt180) cc_final: 0.8471 (mtt180) REVERT: X 95 HIS cc_start: 0.7167 (m90) cc_final: 0.6553 (m-70) REVERT: X 124 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: X 183 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8471 (ptmm) REVERT: Y 98 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8319 (tm-30) REVERT: Y 175 ARG cc_start: 0.8418 (mtm110) cc_final: 0.8125 (mtp-110) REVERT: Y 213 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7997 (m-40) REVERT: Z 137 ASP cc_start: 0.7630 (m-30) cc_final: 0.7384 (m-30) REVERT: Z 164 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7336 (tp30) REVERT: Z 246 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6258 (tt0) REVERT: a 98 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6401 (tm-30) REVERT: a 202 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.5964 (pm20) REVERT: b 106 ASP cc_start: 0.7890 (m-30) cc_final: 0.7619 (m-30) REVERT: b 114 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8657 (mtm) REVERT: b 140 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7635 (tp30) outliers start: 204 outliers final: 77 residues processed: 820 average time/residue: 1.5523 time to fit residues: 1595.1990 Evaluate side-chains 768 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 652 time to evaluate : 5.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 83 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 172 GLU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 202 ASP Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 153 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain T residue 211 MET Chi-restraints excluded: chain T residue 229 GLU Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain U residue 149 SER Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 214 LYS Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 80 ASN Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 213 ASN Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 251 THR Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 201 TRP Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 114 MET Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 5.9990 chunk 330 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 433 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 496 optimal weight: 0.8980 chunk 402 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 297 optimal weight: 0.6980 chunk 522 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 HIS G 59 GLN H 77 ASN I 79 ASN K 124 GLN N 203 GLN ** P 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN Q 39 ASN S 222 GLN T 23 GLN U 92 HIS U 203 GLN V 77 ASN W 79 ASN X 98 ASN Y 124 GLN Y 196 HIS a 148 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 49140 Z= 0.194 Angle : 0.518 22.643 66254 Z= 0.278 Chirality : 0.043 0.179 7400 Planarity : 0.003 0.054 8522 Dihedral : 5.433 92.254 6715 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.27 % Allowed : 17.04 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.11), residues: 6092 helix: 1.92 (0.11), residues: 2208 sheet: 0.64 (0.13), residues: 1392 loop : -0.35 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 280 HIS 0.006 0.001 HIS U 92 PHE 0.033 0.001 PHE P 214 TYR 0.016 0.001 TYR C 21 ARG 0.009 0.000 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 731 time to evaluate : 5.523 Fit side-chains revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8001 (ttmt) REVERT: 3 141 ASP cc_start: 0.5366 (OUTLIER) cc_final: 0.4867 (t0) REVERT: 4 135 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8006 (ttmt) REVERT: A 61 LYS cc_start: 0.7818 (mttm) cc_final: 0.7520 (mtmt) REVERT: A 64 TYR cc_start: 0.8500 (m-80) cc_final: 0.8190 (m-80) REVERT: A 118 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6916 (pt0) REVERT: A 149 TYR cc_start: 0.8821 (p90) cc_final: 0.8450 (p90) REVERT: B 8 GLU cc_start: 0.7926 (tp30) cc_final: 0.7548 (tp30) REVERT: B 174 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7181 (mtp) REVERT: C 24 GLN cc_start: 0.7507 (tt0) cc_final: 0.6749 (tt0) REVERT: C 28 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.5873 (mp10) REVERT: C 37 ASP cc_start: 0.7847 (p0) cc_final: 0.7456 (t0) REVERT: C 40 GLU cc_start: 0.7330 (pt0) cc_final: 0.6703 (pm20) REVERT: C 153 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7055 (tm-30) REVERT: D 17 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6918 (mtm110) REVERT: D 48 GLU cc_start: 0.7925 (pt0) cc_final: 0.7718 (pt0) REVERT: D 65 TYR cc_start: 0.8471 (m-80) cc_final: 0.8250 (m-80) REVERT: D 176 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7346 (mtm) REVERT: D 203 LYS cc_start: 0.6749 (mttt) cc_final: 0.6078 (tttm) REVERT: E 43 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6005 (p90) REVERT: F 23 GLN cc_start: 0.8815 (tp40) cc_final: 0.8535 (mm-40) REVERT: F 70 PHE cc_start: 0.8169 (p90) cc_final: 0.7441 (p90) REVERT: G 214 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: H 97 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8222 (mm110) REVERT: H 151 MET cc_start: 0.8809 (mtm) cc_final: 0.8581 (mtm) REVERT: H 196 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5449 (mppt) REVERT: I 116 ASP cc_start: 0.7478 (t70) cc_final: 0.7146 (t0) REVERT: I 195 TYR cc_start: 0.9328 (p90) cc_final: 0.8655 (p90) REVERT: J 159 GLN cc_start: 0.8368 (mt0) cc_final: 0.8145 (mt0) REVERT: K 98 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8386 (tm-30) REVERT: K 175 ARG cc_start: 0.8423 (mtp-110) cc_final: 0.8131 (mtp-110) REVERT: L 137 ASP cc_start: 0.7661 (m-30) cc_final: 0.7420 (m-30) REVERT: L 161 GLN cc_start: 0.8215 (pp30) cc_final: 0.7963 (mp10) REVERT: L 164 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: L 257 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6842 (m-30) REVERT: L 268 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: M 148 ASN cc_start: 0.7714 (p0) cc_final: 0.7359 (p0) REVERT: N 102 MET cc_start: 0.8424 (mmt) cc_final: 0.8138 (mmt) REVERT: N 106 ASP cc_start: 0.7771 (m-30) cc_final: 0.7414 (m-30) REVERT: N 140 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: N 142 GLU cc_start: 0.8016 (tp30) cc_final: 0.7731 (pm20) REVERT: N 193 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.8024 (mtp85) REVERT: O 64 TYR cc_start: 0.8588 (m-80) cc_final: 0.8254 (m-80) REVERT: O 149 TYR cc_start: 0.8831 (p90) cc_final: 0.8316 (p90) REVERT: O 207 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7560 (mp10) REVERT: P 11 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7318 (mtp85) REVERT: P 91 ASP cc_start: 0.8349 (t0) cc_final: 0.8050 (t0) REVERT: P 197 LYS cc_start: 0.7935 (mttt) cc_final: 0.7240 (ptpp) REVERT: Q 20 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6573 (mm-30) REVERT: Q 24 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: Q 64 ASP cc_start: 0.7262 (t0) cc_final: 0.6705 (t0) REVERT: Q 66 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6462 (p0) REVERT: Q 143 TYR cc_start: 0.8523 (m-80) cc_final: 0.8297 (m-80) REVERT: R 50 LYS cc_start: 0.7759 (ttpt) cc_final: 0.7285 (tmmm) REVERT: R 97 GLU cc_start: 0.8468 (tt0) cc_final: 0.8171 (tt0) REVERT: R 111 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: S 30 GLN cc_start: 0.7682 (mt0) cc_final: 0.7436 (mt0) REVERT: S 38 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8139 (mp) REVERT: S 43 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.5919 (p90) REVERT: S 163 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7816 (mtt90) REVERT: S 206 LYS cc_start: 0.7749 (pttt) cc_final: 0.7536 (mtpt) REVERT: T 100 MET cc_start: 0.8724 (mtt) cc_final: 0.8373 (mtm) REVERT: U 145 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7792 (ppp) REVERT: U 177 GLU cc_start: 0.6819 (mp0) cc_final: 0.6510 (mt-10) REVERT: U 186 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: V 97 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8239 (mm110) REVERT: V 151 MET cc_start: 0.8813 (mtm) cc_final: 0.8508 (mtm) REVERT: V 154 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: V 177 ASN cc_start: 0.8737 (m-40) cc_final: 0.8518 (m110) REVERT: V 190 MET cc_start: 0.8116 (mmt) cc_final: 0.7715 (mmp) REVERT: V 196 LYS cc_start: 0.6392 (tptt) cc_final: 0.5357 (mppt) REVERT: W 189 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8848 (tp) REVERT: W 195 TYR cc_start: 0.9330 (p90) cc_final: 0.8709 (p90) REVERT: W 198 ARG cc_start: 0.8707 (mtt180) cc_final: 0.8486 (mtt180) REVERT: X 95 HIS cc_start: 0.7099 (m90) cc_final: 0.6519 (m-70) REVERT: X 124 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8402 (tm-30) REVERT: X 183 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8279 (ptmm) REVERT: Y 98 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8403 (tm-30) REVERT: Y 175 ARG cc_start: 0.8355 (mtm110) cc_final: 0.8111 (mtp-110) REVERT: Z 137 ASP cc_start: 0.7634 (m-30) cc_final: 0.7370 (m-30) REVERT: Z 164 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: Z 246 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6180 (tt0) REVERT: a 98 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6386 (tm-30) REVERT: a 148 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7162 (p0) REVERT: a 202 GLN cc_start: 0.6463 (OUTLIER) cc_final: 0.5838 (pm20) REVERT: b 86 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7163 (tpt-90) REVERT: b 106 ASP cc_start: 0.7822 (m-30) cc_final: 0.7565 (m-30) REVERT: b 140 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7616 (tp30) outliers start: 173 outliers final: 71 residues processed: 834 average time/residue: 1.6037 time to fit residues: 1679.4381 Evaluate side-chains 803 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 698 time to evaluate : 5.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 13 ASP Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 211 MET Chi-restraints excluded: chain T residue 229 GLU Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain U residue 149 SER Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 214 LYS Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 210 MET Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 148 ASN Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 0.8980 chunk 524 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 582 optimal weight: 8.9990 chunk 483 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 112 GLN G 52 HIS G 59 GLN G 120 GLN I 79 ASN K 124 GLN K 150 GLN M 64 ASN N 203 GLN ** P 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN Q 39 ASN R 26 GLN R 188 ASN R 196 ASN U 92 HIS U 120 GLN V 77 ASN W 79 ASN Y 124 GLN Y 150 GLN Z 118 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 49140 Z= 0.452 Angle : 0.631 25.188 66254 Z= 0.333 Chirality : 0.047 0.214 7400 Planarity : 0.004 0.071 8522 Dihedral : 5.733 80.074 6713 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.17 % Allowed : 16.87 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.11), residues: 6092 helix: 1.55 (0.11), residues: 2196 sheet: 0.56 (0.13), residues: 1342 loop : -0.45 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Z 280 HIS 0.010 0.002 HIS G 92 PHE 0.026 0.002 PHE S 94 TYR 0.023 0.002 TYR Z 193 ARG 0.010 0.001 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 673 time to evaluate : 5.771 Fit side-chains revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8025 (ttmt) REVERT: 3 141 ASP cc_start: 0.5427 (OUTLIER) cc_final: 0.4873 (t0) REVERT: 4 135 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: A 118 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6871 (tp30) REVERT: A 149 TYR cc_start: 0.8875 (p90) cc_final: 0.8516 (p90) REVERT: B 8 GLU cc_start: 0.7977 (tp30) cc_final: 0.7650 (tp30) REVERT: B 174 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7201 (mtp) REVERT: B 184 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7365 (tp) REVERT: B 221 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5962 (tm) REVERT: C 28 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.6098 (mp10) REVERT: C 37 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7327 (t0) REVERT: C 40 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6644 (pm20) REVERT: C 153 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7058 (tm-30) REVERT: D 17 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6950 (mtm110) REVERT: D 176 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7368 (mtm) REVERT: D 203 LYS cc_start: 0.6709 (mttt) cc_final: 0.6058 (tttm) REVERT: E 6 ASP cc_start: 0.7135 (m-30) cc_final: 0.6827 (m-30) REVERT: E 43 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.5921 (p90) REVERT: E 183 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8058 (ptmt) REVERT: F 70 PHE cc_start: 0.8218 (p90) cc_final: 0.7473 (p90) REVERT: G 159 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7960 (mpp) REVERT: G 214 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: H 97 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8295 (mm110) REVERT: H 192 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6758 (mmp-170) REVERT: H 196 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5588 (mppt) REVERT: I 116 ASP cc_start: 0.7514 (t70) cc_final: 0.7131 (t0) REVERT: I 195 TYR cc_start: 0.9332 (p90) cc_final: 0.8651 (p90) REVERT: J 183 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8248 (ptmm) REVERT: K 98 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8391 (tm-30) REVERT: K 175 ARG cc_start: 0.8435 (mtp-110) cc_final: 0.8126 (mtp-110) REVERT: L 137 ASP cc_start: 0.7690 (m-30) cc_final: 0.7416 (m-30) REVERT: L 161 GLN cc_start: 0.8279 (pp30) cc_final: 0.7999 (mp10) REVERT: L 164 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: L 202 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: L 268 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: M 148 ASN cc_start: 0.7853 (p0) cc_final: 0.7515 (p0) REVERT: N 102 MET cc_start: 0.8465 (mmt) cc_final: 0.8178 (mmt) REVERT: N 106 ASP cc_start: 0.7738 (m-30) cc_final: 0.7414 (m-30) REVERT: N 140 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: O 48 LEU cc_start: 0.8457 (mm) cc_final: 0.7997 (pp) REVERT: O 78 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: O 149 TYR cc_start: 0.8876 (p90) cc_final: 0.8480 (p90) REVERT: O 207 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: P 11 ARG cc_start: 0.7715 (mtp180) cc_final: 0.7393 (mtp85) REVERT: P 91 ASP cc_start: 0.8447 (t0) cc_final: 0.8187 (t0) REVERT: P 197 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7235 (ptpp) REVERT: Q 24 GLN cc_start: 0.7596 (tt0) cc_final: 0.7037 (tt0) REVERT: Q 64 ASP cc_start: 0.7298 (t0) cc_final: 0.6749 (t0) REVERT: Q 66 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6285 (p0) REVERT: Q 137 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7645 (ttmm) REVERT: R 50 LYS cc_start: 0.7652 (ttpt) cc_final: 0.7253 (tmmm) REVERT: R 97 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: R 111 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: R 208 ASN cc_start: 0.6972 (OUTLIER) cc_final: 0.6454 (m-40) REVERT: S 30 GLN cc_start: 0.7835 (mt0) cc_final: 0.7588 (mt0) REVERT: S 38 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8364 (mp) REVERT: S 43 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.5987 (p90) REVERT: S 163 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7811 (mtt90) REVERT: S 206 LYS cc_start: 0.7851 (pttt) cc_final: 0.7626 (mtpt) REVERT: T 50 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: T 100 MET cc_start: 0.8737 (mtt) cc_final: 0.8257 (mtm) REVERT: U 186 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: V 97 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8304 (mm110) REVERT: V 151 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8601 (mtm) REVERT: V 154 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6984 (tp30) REVERT: V 190 MET cc_start: 0.8375 (mmt) cc_final: 0.8131 (mmt) REVERT: W 132 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: W 189 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8888 (tp) REVERT: X 95 HIS cc_start: 0.7322 (m90) cc_final: 0.6551 (m-70) REVERT: X 124 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8370 (tm-30) REVERT: Y 98 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8398 (tm-30) REVERT: Y 175 ARG cc_start: 0.8402 (mtm110) cc_final: 0.8133 (mtp-110) REVERT: Y 213 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7836 (m-40) REVERT: Z 137 ASP cc_start: 0.7711 (m-30) cc_final: 0.7459 (m-30) REVERT: Z 164 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: Z 246 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6293 (tt0) REVERT: a 98 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6392 (tm-30) REVERT: a 202 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6070 (pm20) REVERT: b 86 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7193 (tpt-90) REVERT: b 102 MET cc_start: 0.8538 (mmt) cc_final: 0.8204 (mmt) REVERT: b 106 ASP cc_start: 0.7858 (m-30) cc_final: 0.7597 (m-30) REVERT: b 140 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7616 (tp30) outliers start: 221 outliers final: 95 residues processed: 812 average time/residue: 1.6227 time to fit residues: 1643.9119 Evaluate side-chains 793 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 651 time to evaluate : 6.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 128 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 202 ASP Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 78 GLN Chi-restraints excluded: chain O residue 207 GLN Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain P residue 197 LYS Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain Q residue 117 LYS Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 137 LYS Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 208 ASN Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain S residue 225 SER Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 211 MET Chi-restraints excluded: chain T residue 229 GLU Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 149 SER Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 125 SER Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 151 MET Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 214 LYS Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 189 LEU Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 133 CYS Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 210 MET Chi-restraints excluded: chain Y residue 213 ASN Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 246 GLU Chi-restraints excluded: chain Z residue 251 THR Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 181 ILE Chi-restraints excluded: chain a residue 201 TRP Chi-restraints excluded: chain a residue 202 GLN Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 114 MET Chi-restraints excluded: chain b residue 140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 331 optimal weight: 7.9990 chunk 425 optimal weight: 0.6980 chunk 329 optimal weight: 6.9990 chunk 490 optimal weight: 0.5980 chunk 325 optimal weight: 50.0000 chunk 580 optimal weight: 0.8980 chunk 363 optimal weight: 0.6980 chunk 353 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 133 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 HIS G 59 GLN G 92 HIS G 203 GLN I 79 ASN K 124 GLN N 203 GLN ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 ASN P 112 GLN R 26 GLN R 208 ASN S 222 GLN U 92 HIS V 77 ASN W 79 ASN Y 124 GLN Y 196 HIS a 148 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 49140 Z= 0.160 Angle : 0.514 22.748 66254 Z= 0.276 Chirality : 0.043 0.176 7400 Planarity : 0.004 0.057 8522 Dihedral : 5.308 65.165 6713 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.04 % Allowed : 18.38 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.11), residues: 6092 helix: 1.90 (0.11), residues: 2214 sheet: 0.67 (0.13), residues: 1380 loop : -0.42 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 280 HIS 0.005 0.001 HIS U 92 PHE 0.023 0.001 PHE K 221 TYR 0.020 0.001 TYR C 21 ARG 0.013 0.000 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 724 time to evaluate : 7.004 Fit side-chains revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7986 (ttmt) REVERT: 3 140 ASP cc_start: 0.5194 (t0) cc_final: 0.4955 (t0) REVERT: 3 141 ASP cc_start: 0.5565 (OUTLIER) cc_final: 0.5046 (t0) REVERT: 4 135 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8089 (ttmt) REVERT: A 61 LYS cc_start: 0.7734 (mttm) cc_final: 0.7426 (mtmt) REVERT: A 118 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6889 (pt0) REVERT: A 149 TYR cc_start: 0.8832 (p90) cc_final: 0.8397 (p90) REVERT: B 8 GLU cc_start: 0.7946 (tp30) cc_final: 0.7583 (tp30) REVERT: B 174 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7088 (mtp) REVERT: B 221 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5977 (tm) REVERT: C 24 GLN cc_start: 0.7452 (tt0) cc_final: 0.6782 (tt0) REVERT: C 28 GLN cc_start: 0.6160 (OUTLIER) cc_final: 0.5869 (mp10) REVERT: C 40 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.7022 (pt0) REVERT: C 153 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7079 (tm-30) REVERT: D 17 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6929 (ptp-170) REVERT: D 121 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6290 (m-30) REVERT: D 203 LYS cc_start: 0.6630 (mttt) cc_final: 0.6103 (tttm) REVERT: E 6 ASP cc_start: 0.7094 (m-30) cc_final: 0.6740 (m-30) REVERT: E 43 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.5943 (p90) REVERT: F 23 GLN cc_start: 0.8814 (tp40) cc_final: 0.8546 (mm-40) REVERT: F 70 PHE cc_start: 0.8093 (p90) cc_final: 0.7439 (p90) REVERT: G 177 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: H 97 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8232 (mm110) REVERT: H 158 GLU cc_start: 0.7636 (tt0) cc_final: 0.7240 (mt-10) REVERT: H 196 LYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5455 (mppt) REVERT: I 116 ASP cc_start: 0.7440 (t70) cc_final: 0.7125 (t0) REVERT: I 195 TYR cc_start: 0.9326 (p90) cc_final: 0.8667 (p90) REVERT: J 159 GLN cc_start: 0.8354 (mt0) cc_final: 0.8130 (mt0) REVERT: J 183 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8290 (ptmm) REVERT: K 98 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8407 (tm-30) REVERT: K 175 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8174 (mtp-110) REVERT: L 137 ASP cc_start: 0.7699 (m-30) cc_final: 0.7435 (m-30) REVERT: L 161 GLN cc_start: 0.8244 (pp30) cc_final: 0.8027 (mp10) REVERT: L 164 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: L 249 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: L 257 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6918 (m-30) REVERT: L 268 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: M 148 ASN cc_start: 0.7748 (p0) cc_final: 0.7392 (p0) REVERT: N 86 ARG cc_start: 0.7756 (ttt90) cc_final: 0.7421 (tpt-90) REVERT: N 102 MET cc_start: 0.8419 (mmt) cc_final: 0.8126 (mmt) REVERT: N 106 ASP cc_start: 0.7758 (m-30) cc_final: 0.7388 (m-30) REVERT: N 140 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: N 142 GLU cc_start: 0.7961 (tp30) cc_final: 0.7739 (pm20) REVERT: O 48 LEU cc_start: 0.8395 (mm) cc_final: 0.7989 (pp) REVERT: O 149 TYR cc_start: 0.8831 (p90) cc_final: 0.8293 (p90) REVERT: O 207 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7690 (mp10) REVERT: P 11 ARG cc_start: 0.7779 (mtp180) cc_final: 0.7355 (mtp85) REVERT: P 91 ASP cc_start: 0.8305 (t0) cc_final: 0.8006 (t0) REVERT: P 176 ARG cc_start: 0.7775 (tpt90) cc_final: 0.7525 (tmt90) REVERT: Q 16 LEU cc_start: 0.7992 (mt) cc_final: 0.7761 (mt) REVERT: Q 20 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6527 (mm-30) REVERT: Q 24 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: Q 64 ASP cc_start: 0.7209 (t0) cc_final: 0.6973 (t0) REVERT: Q 66 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6724 (p0) REVERT: Q 198 MET cc_start: 0.6849 (ptt) cc_final: 0.6334 (pmm) REVERT: R 50 LYS cc_start: 0.7604 (ttpt) cc_final: 0.7192 (tmmm) REVERT: R 97 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: R 111 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7538 (tt0) REVERT: R 208 ASN cc_start: 0.6821 (OUTLIER) cc_final: 0.6497 (m-40) REVERT: S 30 GLN cc_start: 0.7768 (mt0) cc_final: 0.7518 (mt0) REVERT: S 38 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8138 (mp) REVERT: S 43 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.5948 (p90) REVERT: S 135 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8988 (tt) REVERT: S 163 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7847 (mtt90) REVERT: T 100 MET cc_start: 0.8749 (mtt) cc_final: 0.8394 (mtm) REVERT: U 50 GLN cc_start: 0.6120 (OUTLIER) cc_final: 0.5862 (pt0) REVERT: U 145 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7710 (ppp) REVERT: U 177 GLU cc_start: 0.6823 (mp0) cc_final: 0.6541 (mt-10) REVERT: U 186 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: V 97 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8232 (mm110) REVERT: V 154 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: V 190 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7767 (mmp) REVERT: W 189 LEU cc_start: 0.9066 (tm) cc_final: 0.8846 (tp) REVERT: W 195 TYR cc_start: 0.9330 (p90) cc_final: 0.8697 (p90) REVERT: W 198 ARG cc_start: 0.8780 (mtt180) cc_final: 0.8493 (mtt180) REVERT: X 95 HIS cc_start: 0.7215 (m90) cc_final: 0.6566 (m-70) REVERT: X 124 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: X 183 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8345 (ptmm) REVERT: Y 98 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8429 (tm-30) REVERT: Y 172 GLU cc_start: 0.7648 (tt0) cc_final: 0.7448 (tt0) REVERT: Y 175 ARG cc_start: 0.8361 (mtm110) cc_final: 0.8116 (mtp-110) REVERT: Z 137 ASP cc_start: 0.7585 (m-30) cc_final: 0.7344 (m-30) REVERT: Z 164 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: a 1 MET cc_start: 0.8110 (ttt) cc_final: 0.7863 (ttp) REVERT: a 98 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6285 (tm-30) REVERT: a 148 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6769 (p0) REVERT: b 86 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7168 (tpt-90) REVERT: b 106 ASP cc_start: 0.7817 (m-30) cc_final: 0.7559 (m-30) outliers start: 161 outliers final: 68 residues processed: 822 average time/residue: 1.6296 time to fit residues: 1674.9240 Evaluate side-chains 786 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 680 time to evaluate : 5.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 128 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 167 CYS Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 177 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 249 GLU Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 208 ASN Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 167 CYS Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 50 GLN Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 190 MET Chi-restraints excluded: chain V residue 214 LYS Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 148 ASN Chi-restraints excluded: chain b residue 86 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 1.9990 chunk 231 optimal weight: 0.0770 chunk 346 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 368 optimal weight: 20.0000 chunk 395 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 456 optimal weight: 8.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 138 ASN B 112 GLN E 59 GLN G 52 HIS G 59 GLN G 120 GLN I 79 ASN K 124 GLN N 203 GLN ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN R 26 GLN U 92 HIS U 120 GLN V 177 ASN W 79 ASN Y 124 GLN a 148 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 49140 Z= 0.189 Angle : 0.525 23.148 66254 Z= 0.279 Chirality : 0.043 0.184 7400 Planarity : 0.004 0.055 8522 Dihedral : 5.218 58.924 6713 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.93 % Allowed : 19.08 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.11), residues: 6092 helix: 2.02 (0.11), residues: 2204 sheet: 0.77 (0.14), residues: 1354 loop : -0.41 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 280 HIS 0.006 0.001 HIS U 92 PHE 0.028 0.001 PHE E 94 TYR 0.021 0.001 TYR C 21 ARG 0.011 0.000 ARG N 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 695 time to evaluate : 5.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 135 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7938 (ttmt) REVERT: 3 140 ASP cc_start: 0.5240 (t0) cc_final: 0.5030 (t0) REVERT: 3 141 ASP cc_start: 0.5538 (OUTLIER) cc_final: 0.5046 (t0) REVERT: 4 135 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8048 (ttmt) REVERT: A 118 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6898 (pt0) REVERT: A 149 TYR cc_start: 0.8822 (p90) cc_final: 0.8434 (p90) REVERT: A 210 ARG cc_start: 0.8474 (ptm-80) cc_final: 0.8127 (ttp80) REVERT: B 8 GLU cc_start: 0.7945 (tp30) cc_final: 0.7597 (tp30) REVERT: B 174 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7093 (mtp) REVERT: B 176 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7650 (ttt180) REVERT: C 24 GLN cc_start: 0.7521 (tt0) cc_final: 0.6793 (tt0) REVERT: C 28 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.6076 (mp10) REVERT: C 37 ASP cc_start: 0.7610 (p0) cc_final: 0.7339 (t0) REVERT: C 40 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: C 55 ILE cc_start: 0.7367 (mm) cc_final: 0.7102 (mt) REVERT: C 64 ASP cc_start: 0.8577 (p0) cc_final: 0.8367 (p0) REVERT: C 66 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6547 (p0) REVERT: C 148 ASP cc_start: 0.8156 (p0) cc_final: 0.7873 (p0) REVERT: C 153 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6945 (tm-30) REVERT: D 17 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6941 (ptp-170) REVERT: D 48 GLU cc_start: 0.7907 (pt0) cc_final: 0.7700 (pt0) REVERT: D 121 ASP cc_start: 0.6545 (OUTLIER) cc_final: 0.6155 (m-30) REVERT: D 203 LYS cc_start: 0.6644 (mttt) cc_final: 0.6068 (tttm) REVERT: E 43 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.5900 (p90) REVERT: F 70 PHE cc_start: 0.8122 (p90) cc_final: 0.7551 (p90) REVERT: G 14 ASP cc_start: 0.8514 (t70) cc_final: 0.8170 (OUTLIER) REVERT: H 97 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8237 (mm110) REVERT: H 196 LYS cc_start: 0.5714 (OUTLIER) cc_final: 0.5129 (mppt) REVERT: I 116 ASP cc_start: 0.7345 (t70) cc_final: 0.7076 (t0) REVERT: I 195 TYR cc_start: 0.9334 (p90) cc_final: 0.8675 (p90) REVERT: J 124 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: J 183 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8297 (ptmm) REVERT: K 98 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8400 (tm-30) REVERT: K 175 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.8197 (mtp-110) REVERT: L 100 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8435 (p) REVERT: L 137 ASP cc_start: 0.7753 (m-30) cc_final: 0.7476 (m-30) REVERT: L 164 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: L 249 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: L 257 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6918 (m-30) REVERT: L 268 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: M 148 ASN cc_start: 0.7695 (p0) cc_final: 0.7342 (p0) REVERT: N 140 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: N 142 GLU cc_start: 0.8011 (tp30) cc_final: 0.7740 (pm20) REVERT: O 48 LEU cc_start: 0.8408 (mm) cc_final: 0.7899 (pp) REVERT: O 149 TYR cc_start: 0.8808 (p90) cc_final: 0.8288 (p90) REVERT: O 207 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: P 11 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7366 (mtp85) REVERT: P 91 ASP cc_start: 0.8308 (t0) cc_final: 0.8021 (t0) REVERT: Q 16 LEU cc_start: 0.7966 (mt) cc_final: 0.7762 (mt) REVERT: Q 20 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6418 (mm-30) REVERT: Q 24 GLN cc_start: 0.7574 (tt0) cc_final: 0.6992 (tt0) REVERT: Q 64 ASP cc_start: 0.7215 (t0) cc_final: 0.6702 (t0) REVERT: Q 66 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6330 (p0) REVERT: R 50 LYS cc_start: 0.7629 (ttpt) cc_final: 0.7200 (tmmm) REVERT: R 97 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: R 111 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: S 30 GLN cc_start: 0.7763 (mt0) cc_final: 0.7520 (mt0) REVERT: S 38 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8129 (mp) REVERT: S 43 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.5961 (p90) REVERT: S 46 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (m-10) REVERT: S 163 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7844 (mtt90) REVERT: T 100 MET cc_start: 0.8742 (mtt) cc_final: 0.8393 (mtm) REVERT: U 50 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5860 (pt0) REVERT: U 145 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7825 (ppp) REVERT: U 186 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: V 97 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8214 (mm110) REVERT: V 151 MET cc_start: 0.8807 (mtm) cc_final: 0.8528 (mtm) REVERT: V 154 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6689 (tp30) REVERT: V 190 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7777 (mmp) REVERT: W 189 LEU cc_start: 0.9085 (tm) cc_final: 0.8855 (tp) REVERT: X 95 HIS cc_start: 0.7230 (m90) cc_final: 0.6542 (m-70) REVERT: X 124 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: X 183 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8346 (ptmm) REVERT: Y 98 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8401 (tm-30) REVERT: Y 175 ARG cc_start: 0.8435 (mtm110) cc_final: 0.8196 (mtp-110) REVERT: Y 213 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7692 (m-40) REVERT: Z 137 ASP cc_start: 0.7660 (m-30) cc_final: 0.7399 (m-30) REVERT: Z 164 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: a 1 MET cc_start: 0.8097 (ttt) cc_final: 0.7840 (ttp) REVERT: a 98 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6348 (tm-30) REVERT: b 86 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7211 (tpt-90) REVERT: b 106 ASP cc_start: 0.7816 (m-30) cc_final: 0.7556 (m-30) outliers start: 155 outliers final: 75 residues processed: 785 average time/residue: 1.5460 time to fit residues: 1524.8658 Evaluate side-chains 772 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 659 time to evaluate : 6.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 135 LYS Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 128 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 17 ARG Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 167 CYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 92 HIS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 192 SER Chi-restraints excluded: chain L residue 249 GLU Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 207 GLN Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain P residue 139 ASP Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 46 PHE Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 167 CYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 50 GLN Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain U residue 149 SER Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 190 MET Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 47 THR Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 204 CYS Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 124 GLU Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 133 CYS Chi-restraints excluded: chain Y residue 213 ASN Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 275 ASP Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 181 ILE Chi-restraints excluded: chain b residue 83 LEU Chi-restraints excluded: chain b residue 86 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 7.9990 chunk 555 optimal weight: 0.8980 chunk 507 optimal weight: 0.6980 chunk 540 optimal weight: 6.9990 chunk 325 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 424 optimal weight: 0.0030 chunk 165 optimal weight: 6.9990 chunk 488 optimal weight: 1.9990 chunk 511 optimal weight: 0.0980 chunk 538 optimal weight: 0.8980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 112 GLN D 56 GLN G 52 HIS G 59 GLN H 48 GLN I 79 ASN K 124 GLN N 203 GLN ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 ASN P 112 GLN S 222 GLN U 92 HIS ** V 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 48 GLN ** V 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 79 ASN Y 124 GLN Y 204 ASN Z 161 GLN ** a 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 49140 Z= 0.147 Angle : 0.509 22.443 66254 Z= 0.271 Chirality : 0.043 0.185 7400 Planarity : 0.003 0.056 8522 Dihedral : 4.957 58.616 6710 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.53 % Allowed : 19.89 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 6092 helix: 2.16 (0.11), residues: 2216 sheet: 0.85 (0.14), residues: 1372 loop : -0.38 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 280 HIS 0.006 0.001 HIS U 92 PHE 0.023 0.001 PHE K 221 TYR 0.023 0.001 TYR C 21 ARG 0.009 0.000 ARG O 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 728 time to evaluate : 5.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 141 ASP cc_start: 0.5273 (OUTLIER) cc_final: 0.4884 (t0) REVERT: 4 135 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8061 (ttmt) REVERT: A 118 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6942 (pt0) REVERT: A 149 TYR cc_start: 0.8803 (p90) cc_final: 0.8381 (p90) REVERT: B 8 GLU cc_start: 0.7925 (tp30) cc_final: 0.7585 (tp30) REVERT: B 176 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7700 (ttt180) REVERT: C 17 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7517 (mm) REVERT: C 24 GLN cc_start: 0.7440 (tt0) cc_final: 0.6807 (tt0) REVERT: C 37 ASP cc_start: 0.7551 (p0) cc_final: 0.7307 (t0) REVERT: C 40 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6863 (pm20) REVERT: C 79 ASP cc_start: 0.8969 (m-30) cc_final: 0.8517 (m-30) REVERT: C 153 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6896 (tm-30) REVERT: D 121 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6188 (m-30) REVERT: D 203 LYS cc_start: 0.6679 (mttt) cc_final: 0.6035 (tttm) REVERT: E 43 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.5853 (p90) REVERT: F 23 GLN cc_start: 0.8846 (tp40) cc_final: 0.8542 (mm-40) REVERT: F 70 PHE cc_start: 0.8165 (p90) cc_final: 0.7646 (p90) REVERT: G 214 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: H 97 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8169 (mm110) REVERT: H 158 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7148 (mt-10) REVERT: H 196 LYS cc_start: 0.5973 (OUTLIER) cc_final: 0.5243 (mppt) REVERT: I 116 ASP cc_start: 0.7376 (t70) cc_final: 0.7065 (t0) REVERT: I 195 TYR cc_start: 0.9333 (p90) cc_final: 0.8716 (p90) REVERT: J 68 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6811 (tp30) REVERT: J 183 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8330 (ptmm) REVERT: K 98 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8430 (tm-30) REVERT: K 175 ARG cc_start: 0.8469 (mtp-110) cc_final: 0.8238 (mtp-110) REVERT: L 137 ASP cc_start: 0.7741 (m-30) cc_final: 0.7465 (m-30) REVERT: L 164 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7191 (tp30) REVERT: L 257 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6910 (m-30) REVERT: L 268 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: M 148 ASN cc_start: 0.7657 (p0) cc_final: 0.7286 (p0) REVERT: N 86 ARG cc_start: 0.7753 (ttt90) cc_final: 0.7333 (tpt-90) REVERT: N 106 ASP cc_start: 0.7749 (m-30) cc_final: 0.7448 (m-30) REVERT: N 111 TYR cc_start: 0.8885 (m-80) cc_final: 0.8517 (m-80) REVERT: N 140 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: N 142 GLU cc_start: 0.8050 (tp30) cc_final: 0.7727 (pm20) REVERT: O 48 LEU cc_start: 0.8385 (mm) cc_final: 0.7880 (pp) REVERT: O 149 TYR cc_start: 0.8809 (p90) cc_final: 0.8249 (p90) REVERT: O 207 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: P 91 ASP cc_start: 0.8256 (t0) cc_final: 0.7987 (t0) REVERT: Q 13 ASP cc_start: 0.6970 (p0) cc_final: 0.6708 (p0) REVERT: Q 16 LEU cc_start: 0.7937 (mt) cc_final: 0.7717 (mt) REVERT: Q 20 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6676 (mm-30) REVERT: Q 24 GLN cc_start: 0.7543 (tt0) cc_final: 0.7088 (tt0) REVERT: Q 64 ASP cc_start: 0.7163 (t0) cc_final: 0.6756 (t0) REVERT: Q 66 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6366 (p0) REVERT: R 15 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: R 25 MET cc_start: 0.8011 (mmm) cc_final: 0.7258 (mmm) REVERT: R 50 LYS cc_start: 0.7610 (ttpt) cc_final: 0.7167 (tmmm) REVERT: R 97 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: R 111 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: S 30 GLN cc_start: 0.7694 (mt0) cc_final: 0.7474 (mt0) REVERT: S 43 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.6003 (p90) REVERT: S 46 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8602 (m-10) REVERT: S 163 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7821 (mtt90) REVERT: T 23 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8307 (mm-40) REVERT: T 100 MET cc_start: 0.8756 (mtt) cc_final: 0.8227 (mtm) REVERT: U 50 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5820 (pt0) REVERT: U 66 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: U 145 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7848 (ppp) REVERT: U 177 GLU cc_start: 0.6811 (mp0) cc_final: 0.6493 (mt-10) REVERT: U 186 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: V 97 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8215 (mm110) REVERT: V 154 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6758 (tp30) REVERT: V 190 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7732 (mmp) REVERT: V 214 LYS cc_start: 0.7645 (tttt) cc_final: 0.7419 (tttp) REVERT: W 189 LEU cc_start: 0.9054 (tm) cc_final: 0.8825 (tp) REVERT: W 198 ARG cc_start: 0.8737 (mtt180) cc_final: 0.8505 (mtt180) REVERT: X 95 HIS cc_start: 0.7249 (m90) cc_final: 0.6552 (m-70) REVERT: X 183 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8496 (ptmm) REVERT: Y 98 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8374 (tm-30) REVERT: Y 175 ARG cc_start: 0.8449 (mtm110) cc_final: 0.8241 (mtp-110) REVERT: Z 137 ASP cc_start: 0.7650 (m-30) cc_final: 0.7387 (m-30) REVERT: Z 164 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7279 (tp30) REVERT: a 1 MET cc_start: 0.8041 (ttt) cc_final: 0.7797 (ttp) REVERT: a 98 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6260 (tm-30) REVERT: b 86 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7491 (tpt-90) REVERT: b 106 ASP cc_start: 0.7794 (m-30) cc_final: 0.7552 (m-30) REVERT: b 138 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8581 (ttp) outliers start: 134 outliers final: 55 residues processed: 802 average time/residue: 1.5699 time to fit residues: 1578.0858 Evaluate side-chains 763 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 674 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 128 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 167 CYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 68 GLU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 207 GLN Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 46 PHE Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 167 CYS Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain U residue 50 GLN Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 190 MET Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 191 ASN Chi-restraints excluded: chain X residue 132 ILE Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 275 ASP Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 148 ASN Chi-restraints excluded: chain a residue 181 ILE Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 138 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 10.0000 chunk 571 optimal weight: 0.7980 chunk 348 optimal weight: 9.9990 chunk 271 optimal weight: 1.9990 chunk 397 optimal weight: 9.9990 chunk 599 optimal weight: 0.9990 chunk 551 optimal weight: 0.9990 chunk 477 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 368 optimal weight: 20.0000 chunk 292 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 79 ASN A 138 ASN B 112 GLN G 52 HIS G 59 GLN G 92 HIS G 120 GLN I 79 ASN K 124 GLN K 150 GLN N 203 GLN ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 HIS U 120 GLN V 36 ASN V 177 ASN W 79 ASN Y 124 GLN ** a 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 49140 Z= 0.188 Angle : 0.529 22.967 66254 Z= 0.280 Chirality : 0.043 0.211 7400 Planarity : 0.004 0.061 8522 Dihedral : 4.926 58.439 6702 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.17 % Allowed : 20.84 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.11), residues: 6092 helix: 2.15 (0.11), residues: 2216 sheet: 0.85 (0.14), residues: 1376 loop : -0.34 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 201 HIS 0.006 0.001 HIS U 92 PHE 0.029 0.001 PHE S 94 TYR 0.027 0.001 TYR C 21 ARG 0.014 0.000 ARG O 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12184 Ramachandran restraints generated. 6092 Oldfield, 0 Emsley, 6092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 678 time to evaluate : 5.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 141 ASP cc_start: 0.5272 (OUTLIER) cc_final: 0.4888 (t0) REVERT: 4 135 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8074 (ttmt) REVERT: A 118 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: A 149 TYR cc_start: 0.8799 (p90) cc_final: 0.8358 (p90) REVERT: B 8 GLU cc_start: 0.7939 (tp30) cc_final: 0.7585 (tp30) REVERT: B 176 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7732 (ttt180) REVERT: C 17 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7459 (mm) REVERT: C 24 GLN cc_start: 0.7465 (tt0) cc_final: 0.6759 (tt0) REVERT: C 28 GLN cc_start: 0.6167 (mp10) cc_final: 0.5874 (mp10) REVERT: C 37 ASP cc_start: 0.7543 (p0) cc_final: 0.7336 (t0) REVERT: C 40 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: C 66 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6549 (p0) REVERT: C 153 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6921 (tm-30) REVERT: D 17 ARG cc_start: 0.7255 (mtm110) cc_final: 0.6872 (ptp-170) REVERT: D 121 ASP cc_start: 0.6536 (OUTLIER) cc_final: 0.6223 (m-30) REVERT: D 203 LYS cc_start: 0.6581 (mttt) cc_final: 0.6056 (tttm) REVERT: E 43 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.5836 (p90) REVERT: F 23 GLN cc_start: 0.8846 (tp40) cc_final: 0.8594 (mm-40) REVERT: F 70 PHE cc_start: 0.8169 (p90) cc_final: 0.7444 (p90) REVERT: G 214 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: H 97 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8206 (mm110) REVERT: H 154 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6917 (tp30) REVERT: H 155 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7738 (mt-10) REVERT: H 196 LYS cc_start: 0.5812 (OUTLIER) cc_final: 0.5059 (mppt) REVERT: I 116 ASP cc_start: 0.7355 (t70) cc_final: 0.7054 (t0) REVERT: I 195 TYR cc_start: 0.9339 (p90) cc_final: 0.8723 (p90) REVERT: J 68 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6848 (tp30) REVERT: J 183 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8291 (ptmm) REVERT: K 98 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8417 (tm-30) REVERT: K 175 ARG cc_start: 0.8472 (mtp-110) cc_final: 0.8239 (mtp-110) REVERT: L 137 ASP cc_start: 0.7735 (m-30) cc_final: 0.7459 (m-30) REVERT: L 164 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: L 257 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.6952 (m-30) REVERT: L 268 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: M 148 ASN cc_start: 0.7663 (p0) cc_final: 0.7292 (p0) REVERT: N 86 ARG cc_start: 0.7762 (ttt90) cc_final: 0.7322 (tpt-90) REVERT: N 106 ASP cc_start: 0.7736 (m-30) cc_final: 0.7420 (m-30) REVERT: N 140 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: N 142 GLU cc_start: 0.8062 (tp30) cc_final: 0.7734 (pm20) REVERT: O 48 LEU cc_start: 0.8407 (mm) cc_final: 0.7884 (pp) REVERT: O 149 TYR cc_start: 0.8820 (p90) cc_final: 0.8268 (p90) REVERT: O 207 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: P 91 ASP cc_start: 0.8257 (t0) cc_final: 0.7987 (t0) REVERT: Q 20 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6655 (mm-30) REVERT: Q 24 GLN cc_start: 0.7549 (tt0) cc_final: 0.7050 (tt0) REVERT: Q 64 ASP cc_start: 0.7228 (t0) cc_final: 0.6762 (t0) REVERT: Q 66 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6372 (p0) REVERT: R 15 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: R 50 LYS cc_start: 0.7651 (ttpt) cc_final: 0.7210 (tmmm) REVERT: R 97 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: R 111 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: S 30 GLN cc_start: 0.7726 (mt0) cc_final: 0.7482 (mt0) REVERT: S 43 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6005 (p90) REVERT: S 46 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8608 (m-80) REVERT: S 163 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7716 (mtt90) REVERT: S 222 GLN cc_start: 0.7661 (tt0) cc_final: 0.7446 (tt0) REVERT: T 100 MET cc_start: 0.8759 (mtt) cc_final: 0.8277 (mtm) REVERT: U 50 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5857 (pt0) REVERT: U 66 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: U 145 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7909 (ppp) REVERT: U 177 GLU cc_start: 0.6875 (mp0) cc_final: 0.6514 (mt-10) REVERT: U 186 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: V 97 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8227 (mm110) REVERT: V 154 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6646 (tp30) REVERT: V 190 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7650 (mmp) REVERT: V 214 LYS cc_start: 0.7679 (tttt) cc_final: 0.7429 (tttp) REVERT: W 132 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: W 189 LEU cc_start: 0.9065 (tm) cc_final: 0.8838 (tp) REVERT: W 203 ARG cc_start: 0.5722 (ppt-90) cc_final: 0.5208 (tpp-160) REVERT: X 95 HIS cc_start: 0.7126 (m90) cc_final: 0.6549 (m-70) REVERT: X 159 GLN cc_start: 0.8285 (mt0) cc_final: 0.8057 (mt0) REVERT: X 183 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8449 (ptmm) REVERT: Y 98 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8372 (tm-30) REVERT: Y 175 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8258 (mtp-110) REVERT: Z 137 ASP cc_start: 0.7724 (m-30) cc_final: 0.7427 (m-30) REVERT: Z 164 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7319 (tp30) REVERT: a 1 MET cc_start: 0.8070 (ttt) cc_final: 0.7803 (ttp) REVERT: a 98 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6244 (tm-30) REVERT: b 86 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7464 (tpt-90) REVERT: b 102 MET cc_start: 0.8407 (mmp) cc_final: 0.7847 (mmm) REVERT: b 106 ASP cc_start: 0.7845 (m-30) cc_final: 0.7602 (m-30) REVERT: b 138 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8553 (ttt) outliers start: 115 outliers final: 62 residues processed: 744 average time/residue: 1.5961 time to fit residues: 1481.4651 Evaluate side-chains 754 residues out of total 5450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 654 time to evaluate : 5.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 128 ASP Chi-restraints excluded: chain 3 residue 141 ASP Chi-restraints excluded: chain 4 residue 128 ASP Chi-restraints excluded: chain 4 residue 135 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain E residue 43 PHE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 167 CYS Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 192 ARG Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 68 GLU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 133 CYS Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 198 ASN Chi-restraints excluded: chain M residue 201 TRP Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 140 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain O residue 207 GLN Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 89 GLU Chi-restraints excluded: chain Q residue 20 GLU Chi-restraints excluded: chain Q residue 66 ASP Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 43 PHE Chi-restraints excluded: chain S residue 46 PHE Chi-restraints excluded: chain S residue 82 THR Chi-restraints excluded: chain S residue 163 ARG Chi-restraints excluded: chain S residue 167 CYS Chi-restraints excluded: chain S residue 218 GLN Chi-restraints excluded: chain U residue 44 CYS Chi-restraints excluded: chain U residue 50 GLN Chi-restraints excluded: chain U residue 66 TYR Chi-restraints excluded: chain U residue 145 MET Chi-restraints excluded: chain U residue 149 SER Chi-restraints excluded: chain U residue 186 GLU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 131 THR Chi-restraints excluded: chain V residue 154 GLU Chi-restraints excluded: chain V residue 190 MET Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 132 GLU Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 191 ASN Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 181 VAL Chi-restraints excluded: chain X residue 183 LYS Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 67 ARG Chi-restraints excluded: chain Y residue 213 ASN Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 275 ASP Chi-restraints excluded: chain Z residue 292 GLU Chi-restraints excluded: chain a residue 181 ILE Chi-restraints excluded: chain b residue 86 ARG Chi-restraints excluded: chain b residue 138 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 3.9990 chunk 508 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 440 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 478 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 491 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 112 GLN E 27 ASN G 52 HIS G 59 GLN G 120 GLN I 79 ASN K 124 GLN M 206 ASN N 203 GLN ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 ASN U 92 HIS U 120 GLN Y 124 GLN Y 204 ASN Y 217 HIS ** a 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110146 restraints weight = 65270.173| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.93 r_work: 0.3292 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 49140 Z= 0.283 Angle : 0.578 24.714 66254 Z= 0.304 Chirality : 0.045 0.189 7400 Planarity : 0.004 0.062 8522 Dihedral : 5.144 58.866 6702 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.32 % Allowed : 20.82 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.11), residues: 6092 helix: 1.97 (0.11), residues: 2222 sheet: 0.75 (0.14), residues: 1378 loop : -0.39 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 280 HIS 0.007 0.001 HIS G 92 PHE 0.026 0.002 PHE P 214 TYR 0.031 0.002 TYR C 21 ARG 0.014 0.000 ARG O 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21588.73 seconds wall clock time: 387 minutes 14.33 seconds (23234.33 seconds total)