Starting phenix.real_space_refine on Fri Dec 8 07:48:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/12_2023/6wq2_21868.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/12_2023/6wq2_21868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/12_2023/6wq2_21868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/12_2023/6wq2_21868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/12_2023/6wq2_21868.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wq2_21868/12_2023/6wq2_21868.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 448 5.49 5 S 204 5.16 5 C 34757 2.51 5 N 9337 2.21 5 O 11494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 159": "OD1" <-> "OD2" Residue "J PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 159": "OD1" <-> "OD2" Residue "L PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 159": "OD1" <-> "OD2" Residue "N PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 159": "OD1" <-> "OD2" Residue "R PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 93": "OE1" <-> "OE2" Residue "R PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 159": "OD1" <-> "OD2" Residue "a GLU 34": "OE1" <-> "OE2" Residue "a PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 128": "OE1" <-> "OE2" Residue "a PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 199": "OD1" <-> "OD2" Residue "b TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 34": "OE1" <-> "OE2" Residue "b PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 128": "OE1" <-> "OE2" Residue "b ASP 199": "OD1" <-> "OD2" Residue "b GLU 201": "OE1" <-> "OE2" Residue "c TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 34": "OE1" <-> "OE2" Residue "c PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 121": "OE1" <-> "OE2" Residue "c GLU 128": "OE1" <-> "OE2" Residue "c ASP 199": "OD1" <-> "OD2" Residue "c GLU 201": "OE1" <-> "OE2" Residue "d TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 128": "OE1" <-> "OE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 34": "OE1" <-> "OE2" Residue "e PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 199": "OD1" <-> "OD2" Residue "e GLU 201": "OE1" <-> "OE2" Residue "f GLU 34": "OE1" <-> "OE2" Residue "f PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 121": "OE1" <-> "OE2" Residue "f GLU 128": "OE1" <-> "OE2" Residue "f ASP 199": "OD1" <-> "OD2" Residue "f GLU 201": "OE1" <-> "OE2" Residue "g TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 34": "OE1" <-> "OE2" Residue "g PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 121": "OE1" <-> "OE2" Residue "g PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 199": "OD1" <-> "OD2" Residue "h TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 34": "OE1" <-> "OE2" Residue "h ASP 50": "OD1" <-> "OD2" Residue "h PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 128": "OE1" <-> "OE2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 199": "OD1" <-> "OD2" Residue "h GLU 201": "OE1" <-> "OE2" Residue "i TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 199": "OD1" <-> "OD2" Residue "i GLU 201": "OE1" <-> "OE2" Residue "j GLU 34": "OE1" <-> "OE2" Residue "j PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 199": "OD1" <-> "OD2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "k PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 121": "OE1" <-> "OE2" Residue "k PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 199": "OD1" <-> "OD2" Residue "k GLU 201": "OE1" <-> "OE2" Residue "l GLU 34": "OE1" <-> "OE2" Residue "l PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 121": "OE1" <-> "OE2" Residue "l GLU 128": "OE1" <-> "OE2" Residue "l TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 198": "OE1" <-> "OE2" Residue "l ASP 199": "OD1" <-> "OD2" Residue "l GLU 201": "OE1" <-> "OE2" Residue "m TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 199": "OD1" <-> "OD2" Residue "m GLU 201": "OE1" <-> "OE2" Residue "n TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 34": "OE1" <-> "OE2" Residue "n PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 199": "OD1" <-> "OD2" Residue "n GLU 201": "OE1" <-> "OE2" Residue "p TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 128": "OE1" <-> "OE2" Residue "p TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 199": "OD1" <-> "OD2" Residue "r GLU 201": "OE1" <-> "OE2" Residue "t TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 34": "OE1" <-> "OE2" Residue "t TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 128": "OE1" <-> "OE2" Residue "t TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 199": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 56240 Number of models: 1 Model: "" Number of chains: 36 Chain: "1" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 4613 Classifications: {'DNA': 225} Link IDs: {'rna3p': 224} Chain: "2" Number of atoms: 4571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 4571 Classifications: {'DNA': 223} Link IDs: {'rna3p': 222} Chain: "A" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "N" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "T" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1219 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "a" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "b" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "c" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "d" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "f" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "g" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "h" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "i" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "j" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "k" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "l" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "m" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "n" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "p" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "r" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "t" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1549 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 24.71, per 1000 atoms: 0.44 Number of scatterers: 56240 At special positions: 0 Unit cell: (161, 159.6, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 204 16.00 P 448 15.00 O 11494 8.00 N 9337 7.00 C 34757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.84 Conformation dependent library (CDL) restraints added in 7.1 seconds 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11322 Finding SS restraints... Secondary structure from input PDB file: 289 helices and 17 sheets defined 77.3% alpha, 2.2% beta 223 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 14.67 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.845A pdb=" N GLY A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 39 Processing helix chain 'A' and resid 39 through 60 Processing helix chain 'A' and resid 61 through 79 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.539A pdb=" N ILE A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.564A pdb=" N VAL B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 39 through 60 Processing helix chain 'B' and resid 61 through 79 Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.941A pdb=" N GLY C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 39 through 60 Processing helix chain 'C' and resid 61 through 79 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.566A pdb=" N VAL D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 Processing helix chain 'D' and resid 39 through 60 Processing helix chain 'D' and resid 61 through 79 Processing helix chain 'D' and resid 81 through 99 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 150 through 166 Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.775A pdb=" N GLY E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 39 through 60 Processing helix chain 'E' and resid 61 through 79 Processing helix chain 'E' and resid 81 through 99 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 150 through 166 Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.898A pdb=" N GLY F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 39 Processing helix chain 'F' and resid 39 through 60 Processing helix chain 'F' and resid 61 through 79 Processing helix chain 'F' and resid 81 through 99 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 150 through 165 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.865A pdb=" N GLY G 29 " --> pdb=" O ILE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 39 Processing helix chain 'G' and resid 39 through 60 Processing helix chain 'G' and resid 61 through 79 Processing helix chain 'G' and resid 81 through 99 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.503A pdb=" N ILE G 111 " --> pdb=" O PRO G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 166 Processing helix chain 'H' and resid 9 through 29 removed outlier: 3.850A pdb=" N GLY H 29 " --> pdb=" O ILE H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 39 Processing helix chain 'H' and resid 39 through 60 Processing helix chain 'H' and resid 61 through 79 Processing helix chain 'H' and resid 81 through 99 Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 150 through 165 Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.865A pdb=" N GLY I 29 " --> pdb=" O ILE I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 39 Processing helix chain 'I' and resid 39 through 60 Processing helix chain 'I' and resid 61 through 79 Processing helix chain 'I' and resid 81 through 99 Processing helix chain 'I' and resid 107 through 120 Processing helix chain 'I' and resid 150 through 166 Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.858A pdb=" N GLY J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 39 through 60 Processing helix chain 'J' and resid 61 through 79 Processing helix chain 'J' and resid 81 through 99 Processing helix chain 'J' and resid 107 through 120 Processing helix chain 'J' and resid 150 through 165 removed outlier: 3.646A pdb=" N VAL J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.871A pdb=" N GLY K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 39 Processing helix chain 'K' and resid 39 through 60 Processing helix chain 'K' and resid 61 through 79 Processing helix chain 'K' and resid 81 through 99 Processing helix chain 'K' and resid 107 through 120 Processing helix chain 'K' and resid 150 through 166 Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.792A pdb=" N GLY L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 39 removed outlier: 3.667A pdb=" N ILE L 36 " --> pdb=" O ASN L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 60 Processing helix chain 'L' and resid 61 through 79 Processing helix chain 'L' and resid 81 through 99 Processing helix chain 'L' and resid 107 through 120 Processing helix chain 'L' and resid 150 through 165 Processing helix chain 'M' and resid 9 through 29 removed outlier: 3.804A pdb=" N GLY M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 39 Processing helix chain 'M' and resid 39 through 60 Processing helix chain 'M' and resid 61 through 79 Processing helix chain 'M' and resid 81 through 99 Processing helix chain 'M' and resid 107 through 120 removed outlier: 3.538A pdb=" N ILE M 111 " --> pdb=" O PRO M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 166 Processing helix chain 'N' and resid 9 through 29 removed outlier: 3.824A pdb=" N GLY N 29 " --> pdb=" O ILE N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 39 Processing helix chain 'N' and resid 39 through 60 Processing helix chain 'N' and resid 61 through 79 Processing helix chain 'N' and resid 81 through 99 Processing helix chain 'N' and resid 107 through 120 Processing helix chain 'N' and resid 150 through 165 removed outlier: 3.538A pdb=" N VAL N 165 " --> pdb=" O LEU N 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 29 removed outlier: 3.847A pdb=" N GLY P 29 " --> pdb=" O ILE P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 39 Processing helix chain 'P' and resid 39 through 60 Processing helix chain 'P' and resid 61 through 79 Processing helix chain 'P' and resid 81 through 99 Processing helix chain 'P' and resid 107 through 120 Processing helix chain 'P' and resid 150 through 165 Processing helix chain 'R' and resid 9 through 29 removed outlier: 3.810A pdb=" N GLY R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 39 Processing helix chain 'R' and resid 39 through 60 Processing helix chain 'R' and resid 61 through 79 Processing helix chain 'R' and resid 81 through 99 Processing helix chain 'R' and resid 107 through 120 Processing helix chain 'R' and resid 150 through 165 removed outlier: 3.626A pdb=" N VAL R 165 " --> pdb=" O LEU R 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 29 removed outlier: 4.038A pdb=" N GLY T 29 " --> pdb=" O ILE T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 39 removed outlier: 3.608A pdb=" N ASN T 39 " --> pdb=" O SER T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 60 Processing helix chain 'T' and resid 61 through 79 Processing helix chain 'T' and resid 81 through 99 Processing helix chain 'T' and resid 107 through 120 Processing helix chain 'T' and resid 150 through 165 removed outlier: 3.568A pdb=" N VAL T 165 " --> pdb=" O LEU T 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 15 through 33 removed outlier: 4.636A pdb=" N ASN a 30 " --> pdb=" O GLY a 26 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR a 31 " --> pdb=" O ILE a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 72 removed outlier: 4.485A pdb=" N GLU a 54 " --> pdb=" O ASP a 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS a 58 " --> pdb=" O GLU a 54 " (cutoff:3.500A) Proline residue: a 65 - end of helix Processing helix chain 'a' and resid 76 through 90 removed outlier: 3.522A pdb=" N VAL a 90 " --> pdb=" O ALA a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 108 removed outlier: 3.682A pdb=" N LEU a 101 " --> pdb=" O THR a 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 130 removed outlier: 4.117A pdb=" N GLU a 128 " --> pdb=" O ASN a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 138 removed outlier: 3.552A pdb=" N ALA a 134 " --> pdb=" O VAL a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 158 Processing helix chain 'a' and resid 162 through 168 removed outlier: 4.173A pdb=" N ALA a 166 " --> pdb=" O PRO a 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL a 168 " --> pdb=" O SER a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 174 removed outlier: 4.234A pdb=" N VAL a 174 " --> pdb=" O MET a 170 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 202 removed outlier: 3.601A pdb=" N LYS a 195 " --> pdb=" O GLU a 191 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 33 removed outlier: 4.569A pdb=" N ASN b 30 " --> pdb=" O GLY b 26 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR b 31 " --> pdb=" O ILE b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 72 removed outlier: 4.612A pdb=" N GLU b 54 " --> pdb=" O ASP b 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS b 58 " --> pdb=" O GLU b 54 " (cutoff:3.500A) Proline residue: b 65 - end of helix Processing helix chain 'b' and resid 76 through 90 removed outlier: 3.554A pdb=" N VAL b 90 " --> pdb=" O ALA b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 97 through 108 removed outlier: 3.681A pdb=" N LEU b 101 " --> pdb=" O THR b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 111 through 130 removed outlier: 4.051A pdb=" N GLU b 128 " --> pdb=" O ASN b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 138 Processing helix chain 'b' and resid 146 through 158 Processing helix chain 'b' and resid 163 through 168 removed outlier: 3.650A pdb=" N VAL b 168 " --> pdb=" O SER b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 174 removed outlier: 4.132A pdb=" N VAL b 174 " --> pdb=" O MET b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 202 removed outlier: 4.157A pdb=" N SER b 192 " --> pdb=" O SER b 188 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS b 195 " --> pdb=" O GLU b 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 33 removed outlier: 4.391A pdb=" N ASN c 30 " --> pdb=" O GLY c 26 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR c 31 " --> pdb=" O ILE c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 72 removed outlier: 4.554A pdb=" N GLU c 54 " --> pdb=" O ASP c 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS c 58 " --> pdb=" O GLU c 54 " (cutoff:3.500A) Proline residue: c 65 - end of helix Processing helix chain 'c' and resid 76 through 90 removed outlier: 3.507A pdb=" N VAL c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 108 removed outlier: 3.690A pdb=" N LEU c 101 " --> pdb=" O THR c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 130 removed outlier: 3.920A pdb=" N GLU c 128 " --> pdb=" O ASN c 124 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 138 Processing helix chain 'c' and resid 146 through 158 Processing helix chain 'c' and resid 163 through 168 removed outlier: 3.801A pdb=" N VAL c 168 " --> pdb=" O SER c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 168 through 174 removed outlier: 3.951A pdb=" N VAL c 174 " --> pdb=" O MET c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 189 through 202 removed outlier: 3.678A pdb=" N LYS c 195 " --> pdb=" O GLU c 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 33 removed outlier: 4.665A pdb=" N ASN d 30 " --> pdb=" O GLY d 26 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR d 31 " --> pdb=" O ILE d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 72 removed outlier: 4.551A pdb=" N GLU d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) Proline residue: d 65 - end of helix Processing helix chain 'd' and resid 76 through 90 removed outlier: 3.629A pdb=" N VAL d 90 " --> pdb=" O ALA d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 108 removed outlier: 3.805A pdb=" N LEU d 101 " --> pdb=" O THR d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 130 removed outlier: 4.077A pdb=" N GLU d 128 " --> pdb=" O ASN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 138 Processing helix chain 'd' and resid 146 through 158 Processing helix chain 'd' and resid 163 through 168 removed outlier: 3.772A pdb=" N VAL d 168 " --> pdb=" O SER d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 168 through 174 removed outlier: 4.334A pdb=" N VAL d 174 " --> pdb=" O MET d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 removed outlier: 4.113A pdb=" N SER d 192 " --> pdb=" O SER d 188 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 15 through 33 removed outlier: 4.659A pdb=" N ASN e 30 " --> pdb=" O GLY e 26 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR e 31 " --> pdb=" O ILE e 27 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 72 removed outlier: 4.512A pdb=" N GLU e 54 " --> pdb=" O ASP e 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS e 58 " --> pdb=" O GLU e 54 " (cutoff:3.500A) Proline residue: e 65 - end of helix Processing helix chain 'e' and resid 76 through 90 Processing helix chain 'e' and resid 97 through 108 removed outlier: 3.683A pdb=" N LEU e 101 " --> pdb=" O THR e 97 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 130 removed outlier: 4.088A pdb=" N GLU e 128 " --> pdb=" O ASN e 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 138 removed outlier: 3.626A pdb=" N ALA e 134 " --> pdb=" O VAL e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 158 Processing helix chain 'e' and resid 163 through 168 removed outlier: 3.698A pdb=" N VAL e 168 " --> pdb=" O SER e 164 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 174 removed outlier: 4.282A pdb=" N VAL e 174 " --> pdb=" O MET e 170 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 202 removed outlier: 3.580A pdb=" N LYS e 195 " --> pdb=" O GLU e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 33 removed outlier: 4.424A pdb=" N ASN f 30 " --> pdb=" O GLY f 26 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR f 31 " --> pdb=" O ILE f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 72 removed outlier: 4.549A pdb=" N GLU f 54 " --> pdb=" O ASP f 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS f 58 " --> pdb=" O GLU f 54 " (cutoff:3.500A) Proline residue: f 65 - end of helix Processing helix chain 'f' and resid 76 through 90 Processing helix chain 'f' and resid 97 through 108 removed outlier: 3.672A pdb=" N LEU f 101 " --> pdb=" O THR f 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 130 removed outlier: 4.053A pdb=" N GLU f 128 " --> pdb=" O ASN f 124 " (cutoff:3.500A) Processing helix chain 'f' and resid 130 through 138 Processing helix chain 'f' and resid 146 through 158 Processing helix chain 'f' and resid 163 through 168 Processing helix chain 'f' and resid 168 through 174 removed outlier: 4.231A pdb=" N VAL f 174 " --> pdb=" O MET f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 189 through 202 removed outlier: 3.627A pdb=" N LYS f 195 " --> pdb=" O GLU f 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 15 through 33 removed outlier: 4.438A pdb=" N ASN g 30 " --> pdb=" O GLY g 26 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR g 31 " --> pdb=" O ILE g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 72 removed outlier: 4.475A pdb=" N GLU g 54 " --> pdb=" O ASP g 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS g 58 " --> pdb=" O GLU g 54 " (cutoff:3.500A) Proline residue: g 65 - end of helix Processing helix chain 'g' and resid 76 through 90 Processing helix chain 'g' and resid 97 through 108 removed outlier: 3.723A pdb=" N LEU g 101 " --> pdb=" O THR g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 130 removed outlier: 4.100A pdb=" N GLU g 128 " --> pdb=" O ASN g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 138 Processing helix chain 'g' and resid 146 through 158 Processing helix chain 'g' and resid 163 through 168 removed outlier: 3.647A pdb=" N VAL g 168 " --> pdb=" O SER g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 174 removed outlier: 4.182A pdb=" N VAL g 174 " --> pdb=" O MET g 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 189 through 202 removed outlier: 3.666A pdb=" N LYS g 195 " --> pdb=" O GLU g 191 " (cutoff:3.500A) Processing helix chain 'h' and resid 15 through 33 removed outlier: 4.485A pdb=" N ASN h 30 " --> pdb=" O GLY h 26 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR h 31 " --> pdb=" O ILE h 27 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 72 removed outlier: 4.461A pdb=" N GLU h 54 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS h 58 " --> pdb=" O GLU h 54 " (cutoff:3.500A) Proline residue: h 65 - end of helix Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.612A pdb=" N VAL h 90 " --> pdb=" O ALA h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 97 through 108 removed outlier: 3.757A pdb=" N LEU h 101 " --> pdb=" O THR h 97 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 130 removed outlier: 4.039A pdb=" N GLU h 128 " --> pdb=" O ASN h 124 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 138 Processing helix chain 'h' and resid 146 through 158 Processing helix chain 'h' and resid 163 through 168 removed outlier: 3.706A pdb=" N VAL h 168 " --> pdb=" O SER h 164 " (cutoff:3.500A) Processing helix chain 'h' and resid 168 through 174 removed outlier: 4.042A pdb=" N VAL h 174 " --> pdb=" O MET h 170 " (cutoff:3.500A) Processing helix chain 'h' and resid 188 through 202 removed outlier: 4.226A pdb=" N SER h 192 " --> pdb=" O SER h 188 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS h 195 " --> pdb=" O GLU h 191 " (cutoff:3.500A) Processing helix chain 'i' and resid 15 through 33 removed outlier: 4.303A pdb=" N ASN i 30 " --> pdb=" O GLY i 26 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR i 31 " --> pdb=" O ILE i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 72 removed outlier: 4.481A pdb=" N GLU i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS i 58 " --> pdb=" O GLU i 54 " (cutoff:3.500A) Proline residue: i 65 - end of helix Processing helix chain 'i' and resid 76 through 90 removed outlier: 3.578A pdb=" N VAL i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 108 removed outlier: 3.771A pdb=" N LEU i 101 " --> pdb=" O THR i 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 130 removed outlier: 4.068A pdb=" N GLU i 128 " --> pdb=" O ASN i 124 " (cutoff:3.500A) Processing helix chain 'i' and resid 130 through 138 removed outlier: 3.526A pdb=" N ALA i 134 " --> pdb=" O VAL i 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 158 Processing helix chain 'i' and resid 162 through 168 removed outlier: 4.167A pdb=" N ALA i 166 " --> pdb=" O PRO i 162 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL i 168 " --> pdb=" O SER i 164 " (cutoff:3.500A) Processing helix chain 'i' and resid 168 through 174 removed outlier: 4.048A pdb=" N VAL i 174 " --> pdb=" O MET i 170 " (cutoff:3.500A) Processing helix chain 'i' and resid 189 through 202 removed outlier: 3.695A pdb=" N LYS i 195 " --> pdb=" O GLU i 191 " (cutoff:3.500A) Processing helix chain 'j' and resid 15 through 33 removed outlier: 4.449A pdb=" N ASN j 30 " --> pdb=" O GLY j 26 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR j 31 " --> pdb=" O ILE j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 72 removed outlier: 4.478A pdb=" N GLU j 54 " --> pdb=" O ASP j 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS j 58 " --> pdb=" O GLU j 54 " (cutoff:3.500A) Proline residue: j 65 - end of helix Processing helix chain 'j' and resid 76 through 90 Processing helix chain 'j' and resid 97 through 108 removed outlier: 3.786A pdb=" N LEU j 101 " --> pdb=" O THR j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 130 removed outlier: 4.076A pdb=" N GLU j 128 " --> pdb=" O ASN j 124 " (cutoff:3.500A) Processing helix chain 'j' and resid 130 through 138 Processing helix chain 'j' and resid 146 through 158 Processing helix chain 'j' and resid 162 through 168 removed outlier: 4.136A pdb=" N ALA j 166 " --> pdb=" O PRO j 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL j 168 " --> pdb=" O SER j 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 174 removed outlier: 4.145A pdb=" N VAL j 174 " --> pdb=" O MET j 170 " (cutoff:3.500A) Processing helix chain 'j' and resid 189 through 202 removed outlier: 3.708A pdb=" N LYS j 195 " --> pdb=" O GLU j 191 " (cutoff:3.500A) Processing helix chain 'k' and resid 15 through 33 removed outlier: 4.375A pdb=" N ASN k 30 " --> pdb=" O GLY k 26 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR k 31 " --> pdb=" O ILE k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 33 through 72 removed outlier: 4.499A pdb=" N GLU k 54 " --> pdb=" O ASP k 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Proline residue: k 65 - end of helix Processing helix chain 'k' and resid 76 through 90 Processing helix chain 'k' and resid 97 through 108 removed outlier: 3.622A pdb=" N LEU k 101 " --> pdb=" O THR k 97 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 130 removed outlier: 4.124A pdb=" N GLU k 128 " --> pdb=" O ASN k 124 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 138 Processing helix chain 'k' and resid 146 through 158 Processing helix chain 'k' and resid 162 through 168 removed outlier: 4.150A pdb=" N ALA k 166 " --> pdb=" O PRO k 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL k 168 " --> pdb=" O SER k 164 " (cutoff:3.500A) Processing helix chain 'k' and resid 168 through 174 removed outlier: 3.981A pdb=" N VAL k 174 " --> pdb=" O MET k 170 " (cutoff:3.500A) Processing helix chain 'k' and resid 189 through 202 removed outlier: 3.681A pdb=" N LYS k 195 " --> pdb=" O GLU k 191 " (cutoff:3.500A) Processing helix chain 'l' and resid 15 through 33 removed outlier: 4.631A pdb=" N ASN l 30 " --> pdb=" O GLY l 26 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR l 31 " --> pdb=" O ILE l 27 " (cutoff:3.500A) Processing helix chain 'l' and resid 33 through 72 removed outlier: 4.464A pdb=" N GLU l 54 " --> pdb=" O ASP l 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS l 58 " --> pdb=" O GLU l 54 " (cutoff:3.500A) Proline residue: l 65 - end of helix Processing helix chain 'l' and resid 76 through 90 removed outlier: 3.533A pdb=" N VAL l 90 " --> pdb=" O ALA l 86 " (cutoff:3.500A) Processing helix chain 'l' and resid 97 through 108 removed outlier: 3.751A pdb=" N LEU l 101 " --> pdb=" O THR l 97 " (cutoff:3.500A) Processing helix chain 'l' and resid 111 through 130 removed outlier: 4.000A pdb=" N GLU l 128 " --> pdb=" O ASN l 124 " (cutoff:3.500A) Processing helix chain 'l' and resid 130 through 138 Processing helix chain 'l' and resid 146 through 158 Processing helix chain 'l' and resid 162 through 168 removed outlier: 4.231A pdb=" N ALA l 166 " --> pdb=" O PRO l 162 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL l 168 " --> pdb=" O SER l 164 " (cutoff:3.500A) Processing helix chain 'l' and resid 168 through 174 removed outlier: 4.184A pdb=" N VAL l 174 " --> pdb=" O MET l 170 " (cutoff:3.500A) Processing helix chain 'l' and resid 188 through 202 removed outlier: 4.285A pdb=" N SER l 192 " --> pdb=" O SER l 188 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS l 195 " --> pdb=" O GLU l 191 " (cutoff:3.500A) Processing helix chain 'm' and resid 15 through 33 removed outlier: 4.484A pdb=" N ASN m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR m 31 " --> pdb=" O ILE m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 33 through 72 removed outlier: 4.302A pdb=" N GLU m 54 " --> pdb=" O ASP m 50 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS m 58 " --> pdb=" O GLU m 54 " (cutoff:3.500A) Proline residue: m 65 - end of helix Processing helix chain 'm' and resid 76 through 90 removed outlier: 3.529A pdb=" N VAL m 90 " --> pdb=" O ALA m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 108 removed outlier: 3.790A pdb=" N LEU m 101 " --> pdb=" O THR m 97 " (cutoff:3.500A) Processing helix chain 'm' and resid 111 through 130 removed outlier: 4.117A pdb=" N GLU m 128 " --> pdb=" O ASN m 124 " (cutoff:3.500A) Processing helix chain 'm' and resid 130 through 138 Processing helix chain 'm' and resid 146 through 158 Processing helix chain 'm' and resid 163 through 168 removed outlier: 3.612A pdb=" N VAL m 168 " --> pdb=" O SER m 164 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 174 removed outlier: 4.056A pdb=" N VAL m 174 " --> pdb=" O MET m 170 " (cutoff:3.500A) Processing helix chain 'm' and resid 189 through 202 Processing helix chain 'n' and resid 15 through 33 removed outlier: 4.605A pdb=" N ASN n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR n 31 " --> pdb=" O ILE n 27 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 72 removed outlier: 4.490A pdb=" N GLU n 54 " --> pdb=" O ASP n 50 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS n 58 " --> pdb=" O GLU n 54 " (cutoff:3.500A) Proline residue: n 65 - end of helix Processing helix chain 'n' and resid 76 through 90 Processing helix chain 'n' and resid 97 through 108 removed outlier: 3.693A pdb=" N LEU n 101 " --> pdb=" O THR n 97 " (cutoff:3.500A) Processing helix chain 'n' and resid 111 through 130 removed outlier: 4.095A pdb=" N GLU n 128 " --> pdb=" O ASN n 124 " (cutoff:3.500A) Processing helix chain 'n' and resid 130 through 138 Processing helix chain 'n' and resid 146 through 158 Processing helix chain 'n' and resid 163 through 168 removed outlier: 3.594A pdb=" N VAL n 168 " --> pdb=" O SER n 164 " (cutoff:3.500A) Processing helix chain 'n' and resid 168 through 174 removed outlier: 4.203A pdb=" N VAL n 174 " --> pdb=" O MET n 170 " (cutoff:3.500A) Processing helix chain 'n' and resid 188 through 202 removed outlier: 4.229A pdb=" N SER n 192 " --> pdb=" O SER n 188 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS n 195 " --> pdb=" O GLU n 191 " (cutoff:3.500A) Processing helix chain 'p' and resid 15 through 33 removed outlier: 4.548A pdb=" N ASN p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR p 31 " --> pdb=" O ILE p 27 " (cutoff:3.500A) Processing helix chain 'p' and resid 33 through 72 removed outlier: 4.492A pdb=" N GLU p 54 " --> pdb=" O ASP p 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) Proline residue: p 65 - end of helix Processing helix chain 'p' and resid 76 through 89 Processing helix chain 'p' and resid 97 through 108 removed outlier: 3.675A pdb=" N LEU p 101 " --> pdb=" O THR p 97 " (cutoff:3.500A) Processing helix chain 'p' and resid 111 through 130 removed outlier: 3.967A pdb=" N GLU p 128 " --> pdb=" O ASN p 124 " (cutoff:3.500A) Processing helix chain 'p' and resid 130 through 138 removed outlier: 3.546A pdb=" N ALA p 134 " --> pdb=" O VAL p 130 " (cutoff:3.500A) Processing helix chain 'p' and resid 146 through 158 Processing helix chain 'p' and resid 163 through 168 removed outlier: 3.852A pdb=" N VAL p 168 " --> pdb=" O SER p 164 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 174 removed outlier: 4.041A pdb=" N VAL p 174 " --> pdb=" O MET p 170 " (cutoff:3.500A) Processing helix chain 'p' and resid 188 through 202 removed outlier: 4.153A pdb=" N SER p 192 " --> pdb=" O SER p 188 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS p 195 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing helix chain 'r' and resid 15 through 33 removed outlier: 4.497A pdb=" N ASN r 30 " --> pdb=" O GLY r 26 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR r 31 " --> pdb=" O ILE r 27 " (cutoff:3.500A) Processing helix chain 'r' and resid 33 through 72 removed outlier: 4.526A pdb=" N GLU r 54 " --> pdb=" O ASP r 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS r 58 " --> pdb=" O GLU r 54 " (cutoff:3.500A) Proline residue: r 65 - end of helix Processing helix chain 'r' and resid 76 through 90 Processing helix chain 'r' and resid 97 through 108 removed outlier: 3.598A pdb=" N LEU r 101 " --> pdb=" O THR r 97 " (cutoff:3.500A) Processing helix chain 'r' and resid 111 through 130 removed outlier: 4.098A pdb=" N GLU r 128 " --> pdb=" O ASN r 124 " (cutoff:3.500A) Processing helix chain 'r' and resid 130 through 138 Processing helix chain 'r' and resid 146 through 158 Processing helix chain 'r' and resid 163 through 168 removed outlier: 3.826A pdb=" N VAL r 168 " --> pdb=" O SER r 164 " (cutoff:3.500A) Processing helix chain 'r' and resid 168 through 174 removed outlier: 4.275A pdb=" N VAL r 174 " --> pdb=" O MET r 170 " (cutoff:3.500A) Processing helix chain 'r' and resid 189 through 202 removed outlier: 3.720A pdb=" N LYS r 195 " --> pdb=" O GLU r 191 " (cutoff:3.500A) Processing helix chain 't' and resid 15 through 33 removed outlier: 4.387A pdb=" N ASN t 30 " --> pdb=" O GLY t 26 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR t 31 " --> pdb=" O ILE t 27 " (cutoff:3.500A) Processing helix chain 't' and resid 33 through 72 removed outlier: 4.717A pdb=" N GLU t 54 " --> pdb=" O ASP t 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS t 58 " --> pdb=" O GLU t 54 " (cutoff:3.500A) Proline residue: t 65 - end of helix Processing helix chain 't' and resid 76 through 90 Processing helix chain 't' and resid 97 through 108 removed outlier: 3.728A pdb=" N LEU t 101 " --> pdb=" O THR t 97 " (cutoff:3.500A) Processing helix chain 't' and resid 111 through 130 removed outlier: 4.089A pdb=" N GLU t 128 " --> pdb=" O ASN t 124 " (cutoff:3.500A) Processing helix chain 't' and resid 130 through 138 Processing helix chain 't' and resid 146 through 158 Processing helix chain 't' and resid 163 through 168 removed outlier: 3.686A pdb=" N VAL t 168 " --> pdb=" O SER t 164 " (cutoff:3.500A) Processing helix chain 't' and resid 168 through 174 removed outlier: 4.173A pdb=" N VAL t 174 " --> pdb=" O MET t 170 " (cutoff:3.500A) Processing helix chain 't' and resid 188 through 202 removed outlier: 4.285A pdb=" N SER t 192 " --> pdb=" O SER t 188 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS t 195 " --> pdb=" O GLU t 191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 139 Processing sheet with id=AA2, first strand: chain 'B' and resid 135 through 139 Processing sheet with id=AA3, first strand: chain 'C' and resid 135 through 139 Processing sheet with id=AA4, first strand: chain 'D' and resid 135 through 139 Processing sheet with id=AA5, first strand: chain 'E' and resid 135 through 139 Processing sheet with id=AA6, first strand: chain 'F' and resid 135 through 139 Processing sheet with id=AA7, first strand: chain 'G' and resid 135 through 139 Processing sheet with id=AA8, first strand: chain 'H' and resid 135 through 139 Processing sheet with id=AA9, first strand: chain 'I' and resid 135 through 139 Processing sheet with id=AB1, first strand: chain 'J' and resid 135 through 139 Processing sheet with id=AB2, first strand: chain 'K' and resid 135 through 139 Processing sheet with id=AB3, first strand: chain 'L' and resid 135 through 139 Processing sheet with id=AB4, first strand: chain 'M' and resid 135 through 139 Processing sheet with id=AB5, first strand: chain 'N' and resid 135 through 139 Processing sheet with id=AB6, first strand: chain 'P' and resid 135 through 139 Processing sheet with id=AB7, first strand: chain 'R' and resid 135 through 139 Processing sheet with id=AB8, first strand: chain 'T' and resid 135 through 139 3335 hydrogen bonds defined for protein. 10005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 446 hydrogen bonds 892 hydrogen bond angles 0 basepair planarities 223 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 18.21 Time building geometry restraints manager: 25.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10943 1.33 - 1.45: 15731 1.45 - 1.57: 30351 1.57 - 1.69: 894 1.69 - 1.81: 408 Bond restraints: 58327 Sorted by residual: bond pdb=" C SER p 157 " pdb=" N MET p 158 " ideal model delta sigma weight residual 1.327 1.276 0.051 2.86e-02 1.22e+03 3.13e+00 bond pdb=" C THR j 178 " pdb=" N PRO j 179 " ideal model delta sigma weight residual 1.334 1.319 0.014 8.40e-03 1.42e+04 2.87e+00 bond pdb=" C THR p 178 " pdb=" N PRO p 179 " ideal model delta sigma weight residual 1.334 1.320 0.014 8.40e-03 1.42e+04 2.64e+00 bond pdb=" C THR d 178 " pdb=" N PRO d 179 " ideal model delta sigma weight residual 1.334 1.320 0.014 8.40e-03 1.42e+04 2.63e+00 bond pdb=" C THR t 178 " pdb=" N PRO t 179 " ideal model delta sigma weight residual 1.334 1.320 0.013 8.40e-03 1.42e+04 2.57e+00 ... (remaining 58322 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.84: 3263 105.84 - 112.88: 32402 112.88 - 119.91: 19703 119.91 - 126.95: 24322 126.95 - 133.98: 1435 Bond angle restraints: 81125 Sorted by residual: angle pdb=" C SER b 157 " pdb=" N MET b 158 " pdb=" CA MET b 158 " ideal model delta sigma weight residual 122.31 110.99 11.32 2.34e+00 1.83e-01 2.34e+01 angle pdb=" N PRO p 179 " pdb=" CA PRO p 179 " pdb=" C PRO p 179 " ideal model delta sigma weight residual 114.68 110.43 4.25 1.04e+00 9.25e-01 1.67e+01 angle pdb=" N PRO g 179 " pdb=" CA PRO g 179 " pdb=" C PRO g 179 " ideal model delta sigma weight residual 114.68 110.47 4.21 1.04e+00 9.25e-01 1.64e+01 angle pdb=" N PRO d 179 " pdb=" CA PRO d 179 " pdb=" C PRO d 179 " ideal model delta sigma weight residual 114.68 110.60 4.08 1.04e+00 9.25e-01 1.54e+01 angle pdb=" N PRO f 179 " pdb=" CA PRO f 179 " pdb=" C PRO f 179 " ideal model delta sigma weight residual 114.68 110.70 3.98 1.04e+00 9.25e-01 1.46e+01 ... (remaining 81120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 29122 17.87 - 35.75: 3499 35.75 - 53.62: 1115 53.62 - 71.50: 254 71.50 - 89.37: 25 Dihedral angle restraints: 34015 sinusoidal: 16301 harmonic: 17714 Sorted by residual: dihedral pdb=" CA ALA j 73 " pdb=" C ALA j 73 " pdb=" N GLY j 74 " pdb=" CA GLY j 74 " ideal model delta harmonic sigma weight residual 180.00 154.02 25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA m 73 " pdb=" C ALA m 73 " pdb=" N GLY m 74 " pdb=" CA GLY m 74 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ALA l 73 " pdb=" C ALA l 73 " pdb=" N GLY l 74 " pdb=" CA GLY l 74 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 34012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 6937 0.042 - 0.084: 1942 0.084 - 0.126: 449 0.126 - 0.168: 11 0.168 - 0.211: 1 Chirality restraints: 9340 Sorted by residual: chirality pdb=" P DA 2 403 " pdb=" OP1 DA 2 403 " pdb=" OP2 DA 2 403 " pdb=" O5' DA 2 403 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' DT 2 406 " pdb=" C4' DT 2 406 " pdb=" O3' DT 2 406 " pdb=" C2' DT 2 406 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" P DT 2 492 " pdb=" OP1 DT 2 492 " pdb=" OP2 DT 2 492 " pdb=" O5' DT 2 492 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 9337 not shown) Planarity restraints: 8642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT 1 150 " 0.027 2.00e-02 2.50e+03 1.82e-02 8.30e+00 pdb=" N1 DT 1 150 " -0.050 2.00e-02 2.50e+03 pdb=" C2 DT 1 150 " 0.004 2.00e-02 2.50e+03 pdb=" O2 DT 1 150 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT 1 150 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT 1 150 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT 1 150 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DT 1 150 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT 1 150 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT 1 150 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA 2 487 " 0.030 2.00e-02 2.50e+03 1.52e-02 6.34e+00 pdb=" N9 DA 2 487 " -0.036 2.00e-02 2.50e+03 pdb=" C8 DA 2 487 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA 2 487 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA 2 487 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA 2 487 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA 2 487 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA 2 487 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA 2 487 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DA 2 487 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA 2 487 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL n 53 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C VAL n 53 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL n 53 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU n 54 " -0.014 2.00e-02 2.50e+03 ... (remaining 8639 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 999 2.61 - 3.19: 57884 3.19 - 3.76: 102310 3.76 - 4.33: 131727 4.33 - 4.90: 201943 Nonbonded interactions: 494863 Sorted by model distance: nonbonded pdb=" OP1 DA 2 467 " pdb=" OG SER I 12 " model vdw 2.043 2.440 nonbonded pdb=" OP1 DA 2 299 " pdb=" OG SER T 12 " model vdw 2.081 2.440 nonbonded pdb=" OP1 DA 2 383 " pdb=" OG SER F 12 " model vdw 2.087 2.440 nonbonded pdb=" OP1 DA 2 371 " pdb=" OG SER H 12 " model vdw 2.088 2.440 nonbonded pdb=" NE2 HIS H 65 " pdb=" O PHE m 187 " model vdw 2.092 2.520 ... (remaining 494858 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 '1' and resid 8 through 230) selection = chain '2' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 9.350 Check model and map are aligned: 0.770 Set scattering table: 0.490 Process input model: 131.850 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 : 0.005 0.053 58327 Z= 0.315 Angle : 0.709 11.320 81125 Z= 0.420 Chirality : 0.039 0.211 9340 Planarity : 0.005 0.040 8642 Dihedral : 16.892 89.374 22693 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.09), residues: 5950 helix: -1.34 (0.07), residues: 4233 sheet: -1.36 (0.35), residues: 170 loop : -3.08 (0.14), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 117 HIS 0.008 0.001 HIS H 65 PHE 0.023 0.002 PHE b 77 TYR 0.021 0.002 TYR m 45 ARG 0.010 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1737 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1736 time to evaluate : 4.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1737 average time/residue: 0.6192 time to fit residues: 1713.7377 Evaluate side-chains 1215 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1214 time to evaluate : 4.598 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4089 time to fit residues: 6.4804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 539 optimal weight: 50.0000 chunk 484 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 326 optimal weight: 0.4980 chunk 258 optimal weight: 6.9990 chunk 500 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 372 optimal weight: 5.9990 chunk 580 optimal weight: 7.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS B 112 HIS C 30 HIS C 112 HIS ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 24 ASN E 30 HIS E 112 HIS F 112 HIS G 24 ASN G 30 HIS G 65 HIS G 98 ASN H 30 HIS H 113 HIS I 30 HIS I 98 ASN I 112 HIS J 24 ASN J 112 HIS K 30 HIS K 98 ASN K 112 HIS L 30 HIS L 112 HIS M 30 HIS M 79 ASN M 112 HIS N 30 HIS P 98 ASN P 112 HIS R 30 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 HIS ** T 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 HIS a 30 ASN a 180 HIS b 30 ASN c 30 ASN c 57 ASN d 30 ASN e 30 ASN ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 30 ASN f 57 ASN g 30 ASN g 136 GLN h 30 ASN h 39 GLN i 30 ASN i 57 ASN i 180 HIS k 30 ASN l 30 ASN l 39 GLN l 94 HIS l 136 GLN m 30 ASN n 57 ASN p 136 GLN p 180 HIS r 30 ASN r 57 ASN r 180 HIS t 30 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 58327 Z= 0.251 Angle : 0.761 10.472 81125 Z= 0.427 Chirality : 0.042 0.191 9340 Planarity : 0.005 0.056 8642 Dihedral : 17.448 68.279 11966 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.24 % Allowed : 17.21 % Favored : 80.55 % 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 (0.10), residues: 5950 helix: 0.19 (0.07), residues: 4335 sheet: -0.74 (0.33), residues: 170 loop : -2.83 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 117 HIS 0.007 0.001 HIS t 180 PHE 0.048 0.002 PHE K 162 TYR 0.025 0.002 TYR F 17 ARG 0.013 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1616 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1504 time to evaluate : 4.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 58 residues processed: 1547 average time/residue: 0.6612 time to fit residues: 1649.7799 Evaluate side-chains 1286 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1228 time to evaluate : 4.375 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.5111 time to fit residues: 59.5829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 322 optimal weight: 8.9990 chunk 180 optimal weight: 8.9990 chunk 482 optimal weight: 6.9990 chunk 395 optimal weight: 0.9990 chunk 160 optimal weight: 20.0000 chunk 581 optimal weight: 0.5980 chunk 627 optimal weight: 10.0000 chunk 517 optimal weight: 40.0000 chunk 576 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 466 optimal weight: 20.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN I 114 ASN L 52 GLN T 79 ASN ** a 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 180 HIS b 57 ASN c 136 GLN d 39 GLN ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 136 GLN f 180 HIS g 14 ASN ** g 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 136 GLN h 38 GLN h 39 GLN h 124 ASN ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 ASN k 39 GLN k 136 GLN l 39 GLN l 180 HIS n 30 ASN p 30 ASN r 39 GLN t 57 ASN t 136 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 58327 Z= 0.237 Angle : 0.762 13.581 81125 Z= 0.423 Chirality : 0.042 0.245 9340 Planarity : 0.005 0.056 8642 Dihedral : 17.304 63.781 11966 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.10 % Allowed : 21.07 % Favored : 76.83 % 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: -0.20 (0.11), residues: 5950 helix: 0.75 (0.08), residues: 4233 sheet: -0.41 (0.34), residues: 170 loop : -2.53 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 117 HIS 0.010 0.001 HIS l 180 PHE 0.027 0.002 PHE R 115 TYR 0.032 0.002 TYR G 17 ARG 0.012 0.001 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1522 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1417 time to evaluate : 4.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 48 residues processed: 1476 average time/residue: 0.6176 time to fit residues: 1463.3290 Evaluate side-chains 1209 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1161 time to evaluate : 4.599 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4486 time to fit residues: 45.1999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 574 optimal weight: 5.9990 chunk 437 optimal weight: 40.0000 chunk 301 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 390 optimal weight: 20.0000 chunk 583 optimal weight: 20.0000 chunk 617 optimal weight: 0.9980 chunk 304 optimal weight: 5.9990 chunk 552 optimal weight: 40.0000 chunk 166 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN H 52 GLN J 52 GLN K 65 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN d 43 ASN d 180 HIS e 43 ASN ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 39 GLN ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 ASN j 43 ASN k 136 GLN ** n 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 39 GLN ** t 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 58327 Z= 0.244 Angle : 0.777 13.998 81125 Z= 0.430 Chirality : 0.042 0.322 9340 Planarity : 0.005 0.055 8642 Dihedral : 17.288 62.017 11966 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.20 % Allowed : 23.49 % Favored : 74.31 % 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: -0.03 (0.11), residues: 5950 helix: 0.86 (0.08), residues: 4233 sheet: None (None), residues: 0 loop : -2.24 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 117 HIS 0.007 0.001 HIS d 180 PHE 0.041 0.002 PHE K 162 TYR 0.028 0.002 TYR a 105 ARG 0.012 0.001 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1438 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1328 time to evaluate : 4.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 50 residues processed: 1376 average time/residue: 0.6504 time to fit residues: 1442.3996 Evaluate side-chains 1184 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1134 time to evaluate : 4.405 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4542 time to fit residues: 48.6850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 514 optimal weight: 30.0000 chunk 350 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 459 optimal weight: 40.0000 chunk 254 optimal weight: 30.0000 chunk 527 optimal weight: 20.0000 chunk 426 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 315 optimal weight: 7.9990 chunk 554 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 overall best weight: 15.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN G 52 GLN G 112 HIS M 114 ASN N 112 HIS ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN d 43 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 39 GLN f 136 GLN g 39 GLN ** g 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 ASN j 57 ASN l 39 GLN ** l 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 43 ASN ** p 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 39 GLN ** r 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 58327 Z= 0.440 Angle : 0.895 13.316 81125 Z= 0.503 Chirality : 0.046 0.225 9340 Planarity : 0.006 0.056 8642 Dihedral : 17.626 68.270 11966 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 32.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.00 % Allowed : 25.85 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.11), residues: 5950 helix: 0.37 (0.08), residues: 4318 sheet: -0.68 (0.35), residues: 170 loop : -2.75 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 117 HIS 0.017 0.002 HIS T 65 PHE 0.028 0.003 PHE R 115 TYR 0.031 0.002 TYR R 17 ARG 0.015 0.001 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1204 time to evaluate : 4.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 78 residues processed: 1262 average time/residue: 0.6254 time to fit residues: 1264.6007 Evaluate side-chains 1146 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1068 time to evaluate : 4.351 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.4302 time to fit residues: 68.0458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 207 optimal weight: 7.9990 chunk 556 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 362 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 618 optimal weight: 7.9990 chunk 513 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 136 GLN h 39 GLN h 124 ASN ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 ASN l 136 GLN n 43 ASN p 43 ASN t 124 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 58327 Z= 0.251 Angle : 0.830 15.240 81125 Z= 0.455 Chirality : 0.043 0.189 9340 Planarity : 0.005 0.078 8642 Dihedral : 17.417 64.575 11966 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.50 % Allowed : 27.41 % Favored : 71.09 % 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: -0.40 (0.11), residues: 5950 helix: 0.57 (0.08), residues: 4318 sheet: -0.38 (0.36), residues: 170 loop : -2.69 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 117 HIS 0.011 0.001 HIS n 180 PHE 0.023 0.002 PHE b 77 TYR 0.025 0.002 TYR G 17 ARG 0.019 0.001 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1266 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 35 residues processed: 1297 average time/residue: 0.6754 time to fit residues: 1415.6823 Evaluate side-chains 1121 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1086 time to evaluate : 4.338 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4841 time to fit residues: 36.5824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 596 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 352 optimal weight: 40.0000 chunk 451 optimal weight: 50.0000 chunk 349 optimal weight: 9.9990 chunk 520 optimal weight: 4.9990 chunk 345 optimal weight: 7.9990 chunk 615 optimal weight: 30.0000 chunk 385 optimal weight: 8.9990 chunk 375 optimal weight: 30.0000 chunk 284 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 HIS ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN J 52 GLN ** J 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 GLN h 125 GLN i 39 GLN j 43 ASN ** n 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 180 HIS ** r 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 180 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 58327 Z= 0.271 Angle : 0.860 15.796 81125 Z= 0.471 Chirality : 0.044 0.241 9340 Planarity : 0.005 0.055 8642 Dihedral : 17.384 62.166 11966 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.38 % Allowed : 29.57 % Favored : 69.05 % 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: -0.43 (0.11), residues: 5950 helix: 0.46 (0.08), residues: 4369 sheet: -0.20 (0.36), residues: 170 loop : -2.52 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 117 HIS 0.016 0.001 HIS n 180 PHE 0.026 0.002 PHE m 100 TYR 0.027 0.002 TYR I 99 ARG 0.014 0.001 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1228 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 30 residues processed: 1255 average time/residue: 0.6319 time to fit residues: 1266.0531 Evaluate side-chains 1115 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1085 time to evaluate : 4.386 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4938 time to fit residues: 31.7454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 381 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 367 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 119 optimal weight: 40.0000 chunk 391 optimal weight: 10.0000 chunk 419 optimal weight: 30.0000 chunk 304 optimal weight: 8.9990 chunk 57 optimal weight: 40.0000 chunk 484 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 ASN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 ASN c 43 ASN ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 136 GLN ** g 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 124 ASN ** n 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 43 ASN ** r 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 58327 Z= 0.277 Angle : 0.895 17.870 81125 Z= 0.488 Chirality : 0.044 0.230 9340 Planarity : 0.005 0.057 8642 Dihedral : 17.387 61.353 11966 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.52 % Allowed : 30.51 % Favored : 67.97 % 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: -0.55 (0.11), residues: 5950 helix: 0.37 (0.08), residues: 4335 sheet: -0.27 (0.36), residues: 170 loop : -2.48 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 117 HIS 0.010 0.001 HIS R 65 PHE 0.033 0.002 PHE G 162 TYR 0.028 0.002 TYR I 99 ARG 0.014 0.001 ARG H 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1176 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 39 residues processed: 1200 average time/residue: 0.6271 time to fit residues: 1213.4174 Evaluate side-chains 1117 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1078 time to evaluate : 4.378 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4447 time to fit residues: 37.6862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 560 optimal weight: 3.9990 chunk 590 optimal weight: 10.0000 chunk 538 optimal weight: 5.9990 chunk 573 optimal weight: 6.9990 chunk 589 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 chunk 250 optimal weight: 7.9990 chunk 450 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 518 optimal weight: 0.0980 chunk 542 optimal weight: 9.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 39 GLN ** l 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 14 ASN p 38 GLN r 43 ASN r 124 ASN ** r 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 58327 Z= 0.262 Angle : 0.910 15.501 81125 Z= 0.493 Chirality : 0.045 0.232 9340 Planarity : 0.005 0.058 8642 Dihedral : 17.346 69.599 11966 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 25.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.86 % Allowed : 30.99 % Favored : 68.15 % 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: -0.57 (0.11), residues: 5950 helix: 0.27 (0.08), residues: 4420 sheet: 0.21 (0.34), residues: 204 loop : -2.49 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 117 HIS 0.012 0.001 HIS R 65 PHE 0.034 0.002 PHE C 134 TYR 0.031 0.002 TYR G 17 ARG 0.016 0.001 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1173 time to evaluate : 4.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 1186 average time/residue: 0.6333 time to fit residues: 1202.9660 Evaluate side-chains 1094 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1072 time to evaluate : 4.323 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4620 time to fit residues: 23.8470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 571 optimal weight: 5.9990 chunk 376 optimal weight: 0.0980 chunk 606 optimal weight: 8.9990 chunk 370 optimal weight: 7.9990 chunk 287 optimal weight: 0.9980 chunk 421 optimal weight: 9.9990 chunk 636 optimal weight: 3.9990 chunk 585 optimal weight: 8.9990 chunk 506 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 391 optimal weight: 0.4980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 ASN ** J 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 HIS ** M 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN P 112 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 180 HIS ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 124 ASN g 136 GLN h 180 HIS p 14 ASN r 43 ASN ** r 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 58327 Z= 0.252 Angle : 0.950 15.435 81125 Z= 0.511 Chirality : 0.046 0.281 9340 Planarity : 0.005 0.057 8642 Dihedral : 17.289 87.398 11966 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.52 % Allowed : 32.13 % Favored : 67.35 % 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: 5950 helix: 0.23 (0.08), residues: 4369 sheet: 0.35 (0.34), residues: 204 loop : -2.59 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 117 HIS 0.017 0.001 HIS h 180 PHE 0.041 0.002 PHE D 162 TYR 0.046 0.002 TYR R 17 ARG 0.017 0.001 ARG D 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11900 Ramachandran restraints generated. 5950 Oldfield, 0 Emsley, 5950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1209 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 1217 average time/residue: 0.6505 time to fit residues: 1273.7215 Evaluate side-chains 1125 residues out of total 5168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1117 time to evaluate : 4.347 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4431 time to fit residues: 12.3382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 639 random chunks: chunk 310 optimal weight: 7.9990 chunk 402 optimal weight: 8.9990 chunk 540 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 467 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 507 optimal weight: 30.0000 chunk 212 optimal weight: 5.9990 chunk 521 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 180 HIS ** b 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 136 GLN ** g 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 124 ASN ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 ASN ** i 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 38 GLN ** t 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.048048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.040563 restraints weight = 406383.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.041678 restraints weight = 215213.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.042385 restraints weight = 145188.438| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 58327 Z= 0.293 Angle : 0.972 16.112 81125 Z= 0.528 Chirality : 0.047 0.267 9340 Planarity : 0.005 0.058 8642 Dihedral : 17.365 87.561 11966 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 27.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.70 % Allowed : 32.49 % Favored : 66.81 % 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: -0.81 (0.11), residues: 5950 helix: 0.09 (0.08), residues: 4386 sheet: 0.36 (0.34), residues: 204 loop : -2.50 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 117 HIS 0.017 0.001 HIS i 180 PHE 0.040 0.002 PHE D 162 TYR 0.042 0.002 TYR f 45 ARG 0.022 0.001 ARG D 44 =============================================================================== Job complete usr+sys time: 17798.95 seconds wall clock time: 311 minutes 34.88 seconds (18694.88 seconds total)