Starting phenix.real_space_refine on Sun Mar 24 09:08:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5r_30993/03_2024/7e5r_30993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5r_30993/03_2024/7e5r_30993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5r_30993/03_2024/7e5r_30993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5r_30993/03_2024/7e5r_30993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5r_30993/03_2024/7e5r_30993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5r_30993/03_2024/7e5r_30993.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 25806 2.51 5 N 6759 2.21 5 O 7950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ASP 40": "OD1" <-> "OD2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 77": "OD1" <-> "OD2" Residue "L TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 40": "OD1" <-> "OD2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 77": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 40": "OD1" <-> "OD2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 77": "OD1" <-> "OD2" Residue "O TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "M PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "U ASP 1": "OD1" <-> "OD2" Residue "U PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 81": "OE1" <-> "OE2" Residue "U ASP 82": "OD1" <-> "OD2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 98": "NH1" <-> "NH2" Residue "V ASP 1": "OD1" <-> "OD2" Residue "V PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 81": "OE1" <-> "OE2" Residue "V ASP 82": "OD1" <-> "OD2" Residue "V TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "K ASP 1": "OD1" <-> "OD2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ASP 61": "OD1" <-> "OD2" Residue "R ASP 83": "OD1" <-> "OD2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 55": "OE1" <-> "OE2" Residue "W ARG 68": "NH1" <-> "NH2" Residue "W ASP 74": "OD1" <-> "OD2" Residue "W TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 83": "OE1" <-> "OE2" Residue "W GLU 90": "OE1" <-> "OE2" Residue "W ASP 91": "OD1" <-> "OD2" Residue "W PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "S ASP 61": "OD1" <-> "OD2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "X ARG 20": "NH1" <-> "NH2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 55": "OE1" <-> "OE2" Residue "X ARG 68": "NH1" <-> "NH2" Residue "X ASP 74": "OD1" <-> "OD2" Residue "X TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 83": "OE1" <-> "OE2" Residue "X GLU 90": "OE1" <-> "OE2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ASP 61": "OD1" <-> "OD2" Residue "Q ASP 83": "OD1" <-> "OD2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P ASP 74": "OD1" <-> "OD2" Residue "P TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "P GLU 90": "OE1" <-> "OE2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 808": "OD1" <-> "OD2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40683 Number of models: 1 Model: "" Number of chains: 36 Chain: "H" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "N" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "O" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8360 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "M" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "T" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8360 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "W" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "S" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "Q" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 788 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "P" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "C" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8360 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 53, 'TRANS': 1018} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 21.28, per 1000 atoms: 0.52 Number of scatterers: 40683 At special positions: 0 Unit cell: (217.36, 212.16, 206.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 7950 8.00 N 6759 7.00 C 25806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 89 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 97 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 89 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 97 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG Y 1 " - " ASN A1098 " " NAG Z 1 " - " ASN A1134 " " NAG a 1 " - " ASN B 234 " " NAG b 1 " - " ASN B 717 " " NAG c 1 " - " ASN B 801 " " NAG d 1 " - " ASN B1098 " " NAG e 1 " - " ASN B1134 " " NAG f 1 " - " ASN C 234 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 15.95 Conformation dependent library (CDL) restraints added in 7.3 seconds 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9732 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 93 sheets defined 16.8% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.526A pdb=" N ASN L 31 " --> pdb=" O SER L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.533A pdb=" N THR L 91 " --> pdb=" O SER L 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.526A pdb=" N ASN N 31 " --> pdb=" O SER N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.533A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.526A pdb=" N ASN O 31 " --> pdb=" O SER O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.533A pdb=" N THR O 91 " --> pdb=" O SER O 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.240A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.011A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.743A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.973A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.118A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.831A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.802A pdb=" N PHE U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 76 No H-bonds generated for 'chain 'T' and resid 74 through 76' Processing helix chain 'T' and resid 87 through 91 Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.803A pdb=" N PHE V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.801A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.241A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.010A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.742A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.973A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.119A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.832A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 84 removed outlier: 4.105A pdb=" N GLU R 84 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 33 removed outlier: 3.668A pdb=" N GLU W 32 " --> pdb=" O THR W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 66 removed outlier: 3.791A pdb=" N GLN W 66 " --> pdb=" O GLN W 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 removed outlier: 4.105A pdb=" N GLU S 84 " --> pdb=" O THR S 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 33 removed outlier: 3.668A pdb=" N GLU X 32 " --> pdb=" O THR X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 66 removed outlier: 3.791A pdb=" N GLN X 66 " --> pdb=" O GLN X 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 84 removed outlier: 4.105A pdb=" N GLU Q 84 " --> pdb=" O THR Q 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 33 removed outlier: 3.668A pdb=" N GLU P 32 " --> pdb=" O THR P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 66 removed outlier: 3.790A pdb=" N GLN P 66 " --> pdb=" O GLN P 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.239A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.011A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.743A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.973A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.118A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.832A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.676A pdb=" N VAL H 12 " --> pdb=" O GLU H 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 52 through 53 removed outlier: 5.504A pdb=" N SER H 42 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYS H 38 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.572A pdb=" N ILE L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR L 50 " --> pdb=" O SER L 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.677A pdb=" N VAL D 12 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'D' and resid 52 through 53 removed outlier: 5.504A pdb=" N SER D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS D 38 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.571A pdb=" N ILE N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.676A pdb=" N VAL E 12 " --> pdb=" O GLU E 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'E' and resid 52 through 53 removed outlier: 5.505A pdb=" N SER E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS E 38 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.572A pdb=" N ILE O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR O 50 " --> pdb=" O SER O 59 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.046A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 71 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR A 76 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.039A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.361A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 116 through 121 removed outlier: 4.252A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.580A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.841A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.362A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.128A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1094 through 1096 removed outlier: 4.820A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.513A pdb=" N THR M 113 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR M 59 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER M 52 " --> pdb=" O ASN M 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN M 57 " --> pdb=" O SER M 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.302A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'T' and resid 11 through 12 removed outlier: 3.513A pdb=" N THR T 113 " --> pdb=" O TYR T 94 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET T 34 " --> pdb=" O VAL T 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL T 50 " --> pdb=" O MET T 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR T 59 " --> pdb=" O VAL T 50 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER T 52 " --> pdb=" O ASN T 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASN T 57 " --> pdb=" O SER T 52 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'V' and resid 10 through 13 removed outlier: 6.302A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.513A pdb=" N THR I 113 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR I 59 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER I 52 " --> pdb=" O ASN I 57 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN I 57 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.301A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.046A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.046A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B 71 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR B 76 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.039A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AF3, first strand: chain 'B' and resid 101 through 104 removed outlier: 4.361A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 116 through 121 removed outlier: 4.252A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.581A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.841A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AF8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.362A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AG4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.129A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 1094 through 1096 removed outlier: 4.820A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.526A pdb=" N VAL R 10 " --> pdb=" O THR R 108 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL R 34 " --> pdb=" O TYR R 50 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR R 50 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP R 36 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.526A pdb=" N VAL R 10 " --> pdb=" O THR R 108 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 18 through 23 Processing sheet with id=AG9, first strand: chain 'W' and resid 3 through 4 Processing sheet with id=AH1, first strand: chain 'W' and resid 20 through 23 Processing sheet with id=AH2, first strand: chain 'W' and resid 46 through 49 Processing sheet with id=AH3, first strand: chain 'S' and resid 9 through 12 removed outlier: 6.573A pdb=" N VAL S 10 " --> pdb=" O THR S 108 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 9 through 12 removed outlier: 6.573A pdb=" N VAL S 10 " --> pdb=" O THR S 108 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 18 through 23 Processing sheet with id=AH6, first strand: chain 'X' and resid 3 through 4 Processing sheet with id=AH7, first strand: chain 'X' and resid 20 through 23 Processing sheet with id=AH8, first strand: chain 'X' and resid 46 through 49 Processing sheet with id=AH9, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.526A pdb=" N VAL Q 10 " --> pdb=" O THR Q 108 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR Q 50 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.526A pdb=" N VAL Q 10 " --> pdb=" O THR Q 108 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Q' and resid 18 through 23 Processing sheet with id=AI3, first strand: chain 'P' and resid 3 through 4 Processing sheet with id=AI4, first strand: chain 'P' and resid 20 through 23 Processing sheet with id=AI5, first strand: chain 'P' and resid 46 through 49 Processing sheet with id=AI6, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.047A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.047A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER C 71 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR C 76 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.039A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AJ1, first strand: chain 'C' and resid 101 through 104 removed outlier: 4.362A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 116 through 121 removed outlier: 4.253A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.580A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.840A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AJ6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AJ7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.362A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.818A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.818A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AK2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.129A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'C' and resid 1094 through 1096 removed outlier: 4.819A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) 1536 hydrogen bonds defined for protein. 3978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.82 Time building geometry restraints manager: 17.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12926 1.34 - 1.46: 9129 1.46 - 1.58: 19348 1.58 - 1.70: 0 1.70 - 1.82: 219 Bond restraints: 41622 Sorted by residual: bond pdb=" N ASP N 102 " pdb=" CA ASP N 102 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.05e+01 bond pdb=" N ASP O 102 " pdb=" CA ASP O 102 " ideal model delta sigma weight residual 1.455 1.486 -0.031 7.00e-03 2.04e+04 1.97e+01 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.04e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 ... (remaining 41617 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.83: 1157 106.83 - 113.64: 22961 113.64 - 120.46: 14605 120.46 - 127.27: 17569 127.27 - 134.09: 372 Bond angle restraints: 56664 Sorted by residual: angle pdb=" N THR C 19 " pdb=" CA THR C 19 " pdb=" C THR C 19 " ideal model delta sigma weight residual 112.88 107.08 5.80 1.29e+00 6.01e-01 2.02e+01 angle pdb=" N THR A 19 " pdb=" CA THR A 19 " pdb=" C THR A 19 " ideal model delta sigma weight residual 112.88 107.10 5.78 1.29e+00 6.01e-01 2.00e+01 angle pdb=" N THR B 19 " pdb=" CA THR B 19 " pdb=" C THR B 19 " ideal model delta sigma weight residual 112.88 107.11 5.77 1.29e+00 6.01e-01 2.00e+01 angle pdb=" N TYR L 101 " pdb=" CA TYR L 101 " pdb=" C TYR L 101 " ideal model delta sigma weight residual 112.90 107.45 5.45 1.31e+00 5.83e-01 1.73e+01 angle pdb=" N ASN A 331 " pdb=" CA ASN A 331 " pdb=" C ASN A 331 " ideal model delta sigma weight residual 113.37 107.69 5.68 1.38e+00 5.25e-01 1.70e+01 ... (remaining 56659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 22637 17.77 - 35.55: 1929 35.55 - 53.32: 331 53.32 - 71.09: 77 71.09 - 88.87: 37 Dihedral angle restraints: 25011 sinusoidal: 9795 harmonic: 15216 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.87 -88.87 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.86 -88.86 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.82 -88.82 1 1.00e+01 1.00e-02 9.40e+01 ... (remaining 25008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5319 0.061 - 0.121: 1025 0.121 - 0.182: 100 0.182 - 0.243: 15 0.243 - 0.303: 3 Chirality restraints: 6462 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.68e+01 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.53e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.39e+01 ... (remaining 6459 not shown) Planarity restraints: 7293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG a 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG F 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " 0.341 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG f 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " -0.513 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " 0.086 2.00e-02 2.50e+03 ... (remaining 7290 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 474 2.54 - 3.13: 33300 3.13 - 3.72: 64626 3.72 - 4.31: 91699 4.31 - 4.90: 150412 Nonbonded interactions: 340511 Sorted by model distance: nonbonded pdb=" OD1 ASP L 102 " pdb=" CD PRO L 103 " model vdw 1.953 3.440 nonbonded pdb=" OD1 ASP O 102 " pdb=" CD PRO O 103 " model vdw 2.097 3.440 nonbonded pdb=" OD1 ASP N 102 " pdb=" CD PRO N 103 " model vdw 2.098 3.440 nonbonded pdb=" OG1 THR T 101 " pdb=" OE1 GLU B 484 " model vdw 2.195 2.440 nonbonded pdb=" O ARG B 214 " pdb=" OH TYR B 266 " model vdw 2.200 2.440 ... (remaining 340506 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 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'Y' selection = chain 'Z' selection = 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' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'T' } ncs_group { reference = chain 'K' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' } 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: 4.410 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: 15.800 Check model and map are aligned: 0.540 Set scattering table: 0.360 Process input model: 112.610 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.610 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 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 : 0.004 0.040 41622 Z= 0.229 Angle : 0.680 7.561 56664 Z= 0.382 Chirality : 0.048 0.303 6462 Planarity : 0.008 0.303 7278 Dihedral : 13.498 86.060 15126 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.10 % Favored : 90.74 % Rotamer: Outliers : 0.37 % Allowed : 4.63 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -4.12 (0.09), residues: 5196 helix: -0.83 (0.17), residues: 705 sheet: -2.68 (0.11), residues: 1374 loop : -3.38 (0.09), residues: 3117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 110 HIS 0.009 0.001 HIS A 655 PHE 0.018 0.001 PHE H 82 TYR 0.016 0.001 TYR A 145 ARG 0.004 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 285 time to evaluate : 4.749 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: A 177 MET cc_start: 0.5133 (mmm) cc_final: 0.4634 (mtm) REVERT: A 780 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7312 (mt-10) REVERT: U 15 VAL cc_start: 0.2427 (OUTLIER) cc_final: 0.2102 (p) REVERT: B 153 MET cc_start: 0.9273 (tpt) cc_final: 0.8976 (tpt) REVERT: B 177 MET cc_start: 0.5427 (mmm) cc_final: 0.5033 (mtm) REVERT: B 773 GLU cc_start: 0.7221 (tp30) cc_final: 0.7017 (tp30) REVERT: B 780 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7171 (mt-10) REVERT: B 1029 MET cc_start: 0.7854 (tpp) cc_final: 0.7639 (ttp) REVERT: W 33 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.7045 (m) REVERT: W 65 PHE cc_start: 0.5392 (m-80) cc_final: 0.3816 (m-80) REVERT: W 71 MET cc_start: 0.2168 (mtm) cc_final: 0.0731 (mmm) REVERT: W 95 TYR cc_start: 0.6533 (m-80) cc_final: 0.5979 (m-80) REVERT: Q 88 TYR cc_start: 0.7479 (m-80) cc_final: 0.6845 (m-80) REVERT: P 30 LEU cc_start: 0.5443 (tp) cc_final: 0.5181 (tt) REVERT: P 71 MET cc_start: 0.2915 (mtm) cc_final: 0.0757 (mmm) REVERT: C 557 LYS cc_start: 0.4512 (mttt) cc_final: 0.4075 (mmtt) outliers start: 16 outliers final: 4 residues processed: 301 average time/residue: 0.5822 time to fit residues: 277.0104 Evaluate side-chains 171 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 4.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 438 optimal weight: 4.9990 chunk 393 optimal weight: 50.0000 chunk 218 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 265 optimal weight: 3.9990 chunk 210 optimal weight: 50.0000 chunk 406 optimal weight: 20.0000 chunk 157 optimal weight: 0.2980 chunk 247 optimal weight: 7.9990 chunk 302 optimal weight: 7.9990 chunk 471 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN N 6 GLN O 6 GLN A 121 ASN A 239 GLN A 317 ASN A 334 ASN A 370 ASN A 414 GLN A 487 ASN A 540 ASN A 655 HIS A 703 ASN A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN M 3 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 2 GLN ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN B 239 GLN B 317 ASN B 334 ASN B 370 ASN B 414 GLN B 487 ASN B 540 ASN B 655 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN B 926 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 GLN ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 GLN Q 6 GLN ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN P 114 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 317 ASN C 334 ASN C 370 ASN C 414 GLN C 487 ASN C 540 ASN C 655 HIS C 703 ASN C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN C 926 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 41622 Z= 0.239 Angle : 0.627 9.314 56664 Z= 0.323 Chirality : 0.045 0.297 6462 Planarity : 0.004 0.073 7278 Dihedral : 5.325 50.626 6285 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.53 % Favored : 91.44 % Rotamer: Outliers : 1.14 % Allowed : 9.06 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -3.20 (0.10), residues: 5196 helix: 0.58 (0.19), residues: 711 sheet: -2.25 (0.12), residues: 1404 loop : -2.86 (0.10), residues: 3081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 48 HIS 0.007 0.001 HIS C 655 PHE 0.021 0.001 PHE H 9 TYR 0.024 0.001 TYR X 61 ARG 0.010 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 4.203 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: A 177 MET cc_start: 0.5024 (mmm) cc_final: 0.4348 (mtm) REVERT: A 185 ASN cc_start: 0.5030 (t0) cc_final: 0.4798 (t0) REVERT: B 177 MET cc_start: 0.5612 (mmm) cc_final: 0.5016 (mtm) REVERT: B 185 ASN cc_start: 0.4607 (t0) cc_final: 0.4336 (t0) REVERT: B 773 GLU cc_start: 0.7219 (tp30) cc_final: 0.6917 (tp30) REVERT: B 1029 MET cc_start: 0.7921 (tpp) cc_final: 0.7700 (ttp) REVERT: W 33 VAL cc_start: 0.7209 (OUTLIER) cc_final: 0.7008 (m) REVERT: W 71 MET cc_start: 0.1546 (mtm) cc_final: 0.1115 (mmm) REVERT: X 33 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7127 (m) REVERT: X 71 MET cc_start: 0.3667 (OUTLIER) cc_final: 0.3362 (tpt) REVERT: P 49 MET cc_start: 0.6736 (ptt) cc_final: 0.5205 (ptt) REVERT: P 71 MET cc_start: 0.2604 (mtm) cc_final: 0.0045 (mmm) REVERT: C 557 LYS cc_start: 0.4491 (mttt) cc_final: 0.4131 (mmtt) outliers start: 50 outliers final: 24 residues processed: 223 average time/residue: 0.5607 time to fit residues: 207.2731 Evaluate side-chains 176 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 60 MET Chi-restraints excluded: chain X residue 71 MET Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 743 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 261 optimal weight: 0.0970 chunk 146 optimal weight: 3.9990 chunk 392 optimal weight: 50.0000 chunk 320 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 472 optimal weight: 2.9990 chunk 510 optimal weight: 3.9990 chunk 420 optimal weight: 5.9990 chunk 468 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 378 optimal weight: 40.0000 overall best weight: 1.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 907 ASN A 935 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 901 GLN B 926 GLN B 935 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41622 Z= 0.186 Angle : 0.580 10.997 56664 Z= 0.299 Chirality : 0.043 0.163 6462 Planarity : 0.004 0.062 7278 Dihedral : 5.055 54.155 6281 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.66 % Favored : 92.32 % Rotamer: Outliers : 2.01 % Allowed : 11.48 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -2.66 (0.11), residues: 5196 helix: 1.14 (0.19), residues: 708 sheet: -1.88 (0.12), residues: 1431 loop : -2.53 (0.10), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 110 HIS 0.007 0.001 HIS P 36 PHE 0.018 0.001 PHE H 9 TYR 0.059 0.001 TYR W 61 ARG 0.006 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 168 time to evaluate : 4.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5006 (mmm) cc_final: 0.4506 (mtm) REVERT: A 1029 MET cc_start: 0.8012 (tpp) cc_final: 0.7547 (ttm) REVERT: T 103 MET cc_start: -0.3754 (ptp) cc_final: -0.4526 (ptp) REVERT: B 177 MET cc_start: 0.5169 (mmm) cc_final: 0.4829 (mtm) REVERT: B 178 ASP cc_start: 0.5600 (OUTLIER) cc_final: 0.5150 (p0) REVERT: B 773 GLU cc_start: 0.7319 (tp30) cc_final: 0.7000 (tp30) REVERT: B 901 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: W 71 MET cc_start: 0.2916 (mtm) cc_final: -0.0046 (tmm) REVERT: W 81 TYR cc_start: 0.8521 (m-10) cc_final: 0.8228 (m-10) REVERT: W 82 MET cc_start: 0.4451 (ttt) cc_final: 0.3563 (mtp) REVERT: X 71 MET cc_start: 0.3167 (mmm) cc_final: 0.2654 (tpt) REVERT: P 39 ARG cc_start: 0.6655 (mtt-85) cc_final: 0.5187 (mtt90) REVERT: P 49 MET cc_start: 0.6051 (ptt) cc_final: 0.5424 (ptt) REVERT: P 60 MET cc_start: 0.4134 (OUTLIER) cc_final: 0.2356 (ttt) REVERT: P 71 MET cc_start: 0.1214 (mtm) cc_final: -0.0775 (tpt) REVERT: C 177 MET cc_start: 0.4878 (mmm) cc_final: 0.4374 (mtm) REVERT: C 178 ASP cc_start: 0.5613 (OUTLIER) cc_final: 0.5394 (p0) REVERT: C 557 LYS cc_start: 0.4397 (mttt) cc_final: 0.4071 (mmtt) outliers start: 88 outliers final: 46 residues processed: 241 average time/residue: 0.5092 time to fit residues: 207.2554 Evaluate side-chains 199 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 149 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 60 MET Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 743 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 466 optimal weight: 1.9990 chunk 354 optimal weight: 50.0000 chunk 245 optimal weight: 9.9990 chunk 52 optimal weight: 50.0000 chunk 225 optimal weight: 50.0000 chunk 317 optimal weight: 8.9990 chunk 473 optimal weight: 3.9990 chunk 501 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 449 optimal weight: 50.0000 chunk 135 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 901 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Q 39 GLN C 49 HIS C 81 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 41622 Z= 0.561 Angle : 0.807 12.654 56664 Z= 0.410 Chirality : 0.048 0.261 6462 Planarity : 0.005 0.072 7278 Dihedral : 5.810 59.054 6280 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.28 % Favored : 89.68 % Rotamer: Outliers : 2.83 % Allowed : 13.38 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.11), residues: 5196 helix: 0.45 (0.19), residues: 726 sheet: -2.00 (0.12), residues: 1488 loop : -2.56 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP W 37 HIS 0.008 0.002 HIS C 207 PHE 0.033 0.002 PHE B 306 TYR 0.027 0.002 TYR W 61 ARG 0.008 0.001 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 165 time to evaluate : 4.797 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: H 9 PHE cc_start: 0.4693 (OUTLIER) cc_final: 0.2301 (p90) REVERT: A 1029 MET cc_start: 0.8109 (tpp) cc_final: 0.7681 (ttm) REVERT: B 869 MET cc_start: 0.8170 (mtm) cc_final: 0.7930 (ttm) REVERT: B 901 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8737 (tm130) REVERT: B 1029 MET cc_start: 0.8064 (tpp) cc_final: 0.7729 (ttm) REVERT: W 71 MET cc_start: 0.2831 (mtm) cc_final: -0.0306 (tmm) REVERT: X 71 MET cc_start: 0.3764 (OUTLIER) cc_final: 0.2859 (tpt) REVERT: P 39 ARG cc_start: 0.7057 (mtt-85) cc_final: 0.5612 (mtt90) REVERT: P 49 MET cc_start: 0.6623 (ptt) cc_final: 0.5977 (ptt) outliers start: 124 outliers final: 82 residues processed: 274 average time/residue: 0.5293 time to fit residues: 242.3944 Evaluate side-chains 230 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 145 time to evaluate : 4.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain S residue 50 TYR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 61 TYR Chi-restraints excluded: chain X residue 71 MET Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 417 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 7 optimal weight: 50.0000 chunk 373 optimal weight: 30.0000 chunk 206 optimal weight: 50.0000 chunk 428 optimal weight: 0.6980 chunk 346 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 256 optimal weight: 3.9990 chunk 450 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1002 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 41622 Z= 0.314 Angle : 0.635 11.058 56664 Z= 0.326 Chirality : 0.044 0.226 6462 Planarity : 0.004 0.062 7278 Dihedral : 5.548 58.593 6280 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.60 % Allowed : 15.43 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.11), residues: 5196 helix: 0.87 (0.19), residues: 732 sheet: -1.84 (0.12), residues: 1470 loop : -2.37 (0.10), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W 37 HIS 0.007 0.001 HIS W 36 PHE 0.032 0.002 PHE B 306 TYR 0.023 0.001 TYR W 61 ARG 0.004 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 153 time to evaluate : 4.357 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: H 9 PHE cc_start: 0.4740 (OUTLIER) cc_final: 0.2417 (p90) REVERT: A 1029 MET cc_start: 0.8012 (tpp) cc_final: 0.7748 (ttm) REVERT: B 177 MET cc_start: 0.5322 (mmm) cc_final: 0.5101 (mtm) REVERT: B 178 ASP cc_start: 0.5935 (OUTLIER) cc_final: 0.5657 (p0) REVERT: B 901 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: W 71 MET cc_start: 0.2433 (mtm) cc_final: -0.0560 (tmm) REVERT: W 82 MET cc_start: 0.4707 (ttt) cc_final: 0.3898 (mtp) REVERT: W 83 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7085 (mp0) REVERT: X 71 MET cc_start: 0.4090 (mmm) cc_final: 0.3222 (tpt) REVERT: C 177 MET cc_start: 0.5285 (mmm) cc_final: 0.4706 (mtm) outliers start: 114 outliers final: 78 residues processed: 250 average time/residue: 0.5098 time to fit residues: 215.1691 Evaluate side-chains 229 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 148 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain W residue 56 ASP Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 61 TYR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 168 optimal weight: 0.7980 chunk 451 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 502 optimal weight: 0.9980 chunk 416 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 41 optimal weight: 50.0000 chunk 166 optimal weight: 0.9980 chunk 263 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 901 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 104 ASN V 37 GLN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 41622 Z= 0.168 Angle : 0.569 10.622 56664 Z= 0.294 Chirality : 0.043 0.180 6462 Planarity : 0.004 0.063 7278 Dihedral : 5.074 53.483 6280 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.35 % Allowed : 16.51 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.11), residues: 5196 helix: 1.20 (0.19), residues: 711 sheet: -1.54 (0.13), residues: 1479 loop : -2.15 (0.11), residues: 3006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P 37 HIS 0.004 0.001 HIS L 35 PHE 0.029 0.001 PHE B 306 TYR 0.021 0.001 TYR W 61 ARG 0.005 0.000 ARG R 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 157 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 PHE cc_start: 0.4975 (OUTLIER) cc_final: 0.2603 (p90) REVERT: A 1029 MET cc_start: 0.7900 (tpp) cc_final: 0.7693 (ttm) REVERT: B 178 ASP cc_start: 0.5941 (OUTLIER) cc_final: 0.5732 (p0) REVERT: B 1029 MET cc_start: 0.7902 (tpp) cc_final: 0.7675 (ttm) REVERT: W 65 PHE cc_start: 0.5442 (m-80) cc_final: 0.5190 (m-80) REVERT: W 71 MET cc_start: 0.2186 (mtm) cc_final: 0.1463 (tpp) REVERT: W 83 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7106 (mp0) REVERT: W 95 TYR cc_start: 0.6313 (m-80) cc_final: 0.5998 (m-80) REVERT: X 71 MET cc_start: 0.4137 (mmm) cc_final: 0.3218 (tpt) REVERT: P 49 MET cc_start: 0.6930 (ppp) cc_final: 0.4772 (ppp) outliers start: 103 outliers final: 76 residues processed: 243 average time/residue: 0.4971 time to fit residues: 206.2660 Evaluate side-chains 225 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 147 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain W residue 56 ASP Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 61 TYR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 484 optimal weight: 4.9990 chunk 56 optimal weight: 30.0000 chunk 286 optimal weight: 30.0000 chunk 366 optimal weight: 20.0000 chunk 284 optimal weight: 0.8980 chunk 422 optimal weight: 10.0000 chunk 280 optimal weight: 40.0000 chunk 500 optimal weight: 4.9990 chunk 313 optimal weight: 0.2980 chunk 304 optimal weight: 3.9990 chunk 230 optimal weight: 50.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 901 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN ** T 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 185 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 41622 Z= 0.297 Angle : 0.613 15.592 56664 Z= 0.312 Chirality : 0.043 0.200 6462 Planarity : 0.004 0.062 7278 Dihedral : 4.973 41.588 6280 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.58 % Allowed : 16.83 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.11), residues: 5196 helix: 1.24 (0.19), residues: 732 sheet: -1.49 (0.13), residues: 1500 loop : -2.18 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 37 HIS 0.005 0.001 HIS B 207 PHE 0.048 0.001 PHE A 306 TYR 0.017 0.001 TYR W 61 ARG 0.005 0.000 ARG P 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 148 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.2663 (p90) REVERT: A 1029 MET cc_start: 0.8010 (tpp) cc_final: 0.7768 (ttm) REVERT: W 69 VAL cc_start: -0.0559 (OUTLIER) cc_final: -0.1061 (p) REVERT: W 71 MET cc_start: 0.2147 (mtm) cc_final: 0.1116 (mmm) REVERT: W 83 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7122 (mp0) REVERT: X 39 ARG cc_start: 0.5926 (mpt180) cc_final: 0.5533 (mpt180) REVERT: X 71 MET cc_start: 0.4164 (mmm) cc_final: 0.3235 (tpt) outliers start: 113 outliers final: 87 residues processed: 244 average time/residue: 0.4861 time to fit residues: 205.0174 Evaluate side-chains 226 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 137 time to evaluate : 4.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain W residue 56 ASP Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 61 TYR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 309 optimal weight: 1.9990 chunk 199 optimal weight: 30.0000 chunk 298 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 318 optimal weight: 0.8980 chunk 340 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 46 optimal weight: 50.0000 chunk 393 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 ASN ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 185 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 16 GLN ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41622 Z= 0.216 Angle : 0.572 11.172 56664 Z= 0.295 Chirality : 0.043 0.187 6462 Planarity : 0.004 0.062 7278 Dihedral : 4.827 38.844 6280 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.65 % Allowed : 17.28 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.11), residues: 5196 helix: 1.32 (0.19), residues: 729 sheet: -1.37 (0.13), residues: 1485 loop : -2.09 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 37 HIS 0.005 0.001 HIS X 36 PHE 0.041 0.001 PHE A 306 TYR 0.036 0.001 TYR P 61 ARG 0.009 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 143 time to evaluate : 4.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 PHE cc_start: 0.5107 (OUTLIER) cc_final: 0.2756 (p90) REVERT: H 11 SER cc_start: 0.0688 (OUTLIER) cc_final: -0.0226 (m) REVERT: A 1029 MET cc_start: 0.7949 (tpp) cc_final: 0.7729 (ttm) REVERT: B 1029 MET cc_start: 0.7937 (tpp) cc_final: 0.7639 (ttm) REVERT: W 39 ARG cc_start: 0.6402 (mtt90) cc_final: 0.6178 (mtt90) REVERT: W 71 MET cc_start: 0.2117 (mtm) cc_final: 0.1066 (mmm) REVERT: X 60 MET cc_start: 0.6341 (ptm) cc_final: 0.6108 (ptp) REVERT: X 71 MET cc_start: 0.4131 (mmm) cc_final: 0.3224 (tpt) REVERT: P 60 MET cc_start: 0.2425 (ppp) cc_final: 0.1356 (ppp) outliers start: 116 outliers final: 93 residues processed: 238 average time/residue: 0.4812 time to fit residues: 197.9989 Evaluate side-chains 231 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 136 time to evaluate : 4.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain W residue 56 ASP Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 61 TYR Chi-restraints excluded: chain X residue 101 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 455 optimal weight: 40.0000 chunk 479 optimal weight: 0.8980 chunk 437 optimal weight: 1.9990 chunk 466 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 421 optimal weight: 5.9990 chunk 440 optimal weight: 5.9990 chunk 464 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 41622 Z= 0.304 Angle : 0.622 16.293 56664 Z= 0.316 Chirality : 0.043 0.207 6462 Planarity : 0.004 0.061 7278 Dihedral : 4.937 35.579 6280 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.37 % Allowed : 17.65 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.11), residues: 5196 helix: 1.29 (0.19), residues: 729 sheet: -1.40 (0.13), residues: 1503 loop : -2.10 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 48 HIS 0.011 0.001 HIS P 36 PHE 0.030 0.002 PHE B 306 TYR 0.030 0.001 TYR W 61 ARG 0.018 0.000 ARG P 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 149 time to evaluate : 4.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 9 PHE cc_start: 0.5115 (OUTLIER) cc_final: 0.2884 (p90) REVERT: H 11 SER cc_start: 0.0701 (OUTLIER) cc_final: -0.0205 (m) REVERT: A 185 ASN cc_start: 0.6119 (t0) cc_final: 0.5771 (t0) REVERT: A 1029 MET cc_start: 0.8044 (tpp) cc_final: 0.7808 (ttm) REVERT: B 185 ASN cc_start: 0.5528 (t0) cc_final: 0.5294 (t0) REVERT: B 1029 MET cc_start: 0.7988 (tpp) cc_final: 0.7649 (ttm) REVERT: W 49 MET cc_start: 0.4666 (ptt) cc_final: 0.4347 (ptt) REVERT: W 71 MET cc_start: 0.2036 (mtm) cc_final: 0.1337 (tpt) REVERT: X 60 MET cc_start: 0.6401 (ptm) cc_final: 0.6117 (ptp) REVERT: X 71 MET cc_start: 0.3894 (mmm) cc_final: 0.2998 (tpt) REVERT: P 60 MET cc_start: 0.2592 (ppp) cc_final: 0.1458 (ppp) outliers start: 104 outliers final: 93 residues processed: 233 average time/residue: 0.5035 time to fit residues: 201.8230 Evaluate side-chains 232 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 137 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain W residue 56 ASP Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 61 TYR Chi-restraints excluded: chain X residue 101 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 306 optimal weight: 1.9990 chunk 492 optimal weight: 0.8980 chunk 300 optimal weight: 0.7980 chunk 233 optimal weight: 40.0000 chunk 342 optimal weight: 0.8980 chunk 517 optimal weight: 5.9990 chunk 475 optimal weight: 5.9990 chunk 411 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 3 GLN A 49 HIS A 641 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 41622 Z= 0.179 Angle : 0.570 12.207 56664 Z= 0.292 Chirality : 0.042 0.177 6462 Planarity : 0.004 0.062 7278 Dihedral : 4.705 32.100 6280 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.19 % Allowed : 18.01 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.11), residues: 5196 helix: 1.45 (0.19), residues: 711 sheet: -1.36 (0.13), residues: 1560 loop : -1.97 (0.11), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP W 112 HIS 0.009 0.001 HIS P 36 PHE 0.030 0.001 PHE B 306 TYR 0.029 0.001 TYR W 61 ARG 0.005 0.000 ARG P 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 144 time to evaluate : 4.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 9 PHE cc_start: 0.5253 (OUTLIER) cc_final: 0.3023 (p90) REVERT: H 11 SER cc_start: 0.0527 (OUTLIER) cc_final: -0.0357 (m) REVERT: A 185 ASN cc_start: 0.5971 (t0) cc_final: 0.5651 (t0) REVERT: I 34 MET cc_start: 0.2454 (tpp) cc_final: 0.2013 (tpp) REVERT: B 185 ASN cc_start: 0.5315 (t0) cc_final: 0.5014 (t0) REVERT: B 1029 MET cc_start: 0.7913 (tpp) cc_final: 0.7620 (ttm) REVERT: W 39 ARG cc_start: 0.6410 (mtt90) cc_final: 0.6162 (mtt90) REVERT: W 71 MET cc_start: 0.2526 (mtm) cc_final: 0.2050 (tpp) REVERT: W 83 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6693 (mp0) REVERT: X 60 MET cc_start: 0.6211 (ptm) cc_final: 0.5947 (ptp) REVERT: X 71 MET cc_start: 0.3755 (mmm) cc_final: 0.2949 (tpt) REVERT: P 60 MET cc_start: 0.2747 (ppp) cc_final: 0.1654 (ppp) REVERT: P 71 MET cc_start: 0.3004 (tpt) cc_final: 0.2493 (mmm) outliers start: 96 outliers final: 83 residues processed: 222 average time/residue: 0.4823 time to fit residues: 188.7928 Evaluate side-chains 224 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 139 time to evaluate : 4.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 PHE Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain U residue 49 TYR Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain W residue 56 ASP Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain X residue 49 MET Chi-restraints excluded: chain X residue 61 TYR Chi-restraints excluded: chain X residue 101 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 65 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 519 random chunks: chunk 327 optimal weight: 2.9990 chunk 438 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 379 optimal weight: 0.0030 chunk 60 optimal weight: 0.9980 chunk 114 optimal weight: 30.0000 chunk 412 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 423 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 3 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.094480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.063984 restraints weight = 281380.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.063655 restraints weight = 142099.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.064114 restraints weight = 85720.149| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41622 Z= 0.223 Angle : 0.574 12.044 56664 Z= 0.293 Chirality : 0.043 0.185 6462 Planarity : 0.004 0.062 7278 Dihedral : 4.638 31.324 6280 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.10 % Allowed : 17.97 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.11), residues: 5196 helix: 1.46 (0.19), residues: 729 sheet: -1.25 (0.13), residues: 1545 loop : -2.00 (0.11), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 110 HIS 0.008 0.001 HIS P 36 PHE 0.030 0.001 PHE B 306 TYR 0.031 0.001 TYR W 61 ARG 0.007 0.000 ARG C 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7536.82 seconds wall clock time: 139 minutes 28.25 seconds (8368.25 seconds total)