Starting phenix.real_space_refine on Sat Feb 17 06:32:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmv_0921/02_2024/6lmv_0921.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmv_0921/02_2024/6lmv_0921.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/6lmv_0921/02_2024/6lmv_0921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmv_0921/02_2024/6lmv_0921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmv_0921/02_2024/6lmv_0921.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmv_0921/02_2024/6lmv_0921.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= 0.001 sd= 0.008 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 117 5.16 5 C 11538 2.51 5 N 2943 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 305": "OD1" <-> "OD2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 266": "OD1" <-> "OD2" Residue "C ASP 268": "OD1" <-> "OD2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 125": "OD1" <-> "OD2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 182": "OD1" <-> "OD2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 266": "OD1" <-> "OD2" Residue "D ASP 268": "OD1" <-> "OD2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 305": "OD1" <-> "OD2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "E TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 266": "OD1" <-> "OD2" Residue "E ASP 268": "OD1" <-> "OD2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 182": "OD1" <-> "OD2" Residue "F TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 266": "OD1" <-> "OD2" Residue "F ASP 268": "OD1" <-> "OD2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 305": "OD1" <-> "OD2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 125": "OD1" <-> "OD2" Residue "G PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 182": "OD1" <-> "OD2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 266": "OD1" <-> "OD2" Residue "G ASP 268": "OD1" <-> "OD2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 305": "OD1" <-> "OD2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 125": "OD1" <-> "OD2" Residue "H PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 182": "OD1" <-> "OD2" Residue "H TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 266": "OD1" <-> "OD2" Residue "H ASP 268": "OD1" <-> "OD2" Residue "H TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 305": "OD1" <-> "OD2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 125": "OD1" <-> "OD2" Residue "I PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 182": "OD1" <-> "OD2" Residue "I TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 266": "OD1" <-> "OD2" Residue "I ASP 268": "OD1" <-> "OD2" Residue "I TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 305": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17766 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 9.45, per 1000 atoms: 0.53 Number of scatterers: 17766 At special positions: 0 Unit cell: (138.084, 136.631, 103.2, 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 117 16.00 O 3168 8.00 N 2943 7.00 C 11538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 176 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 176 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 176 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 176 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS I 174 " 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 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 2.9 seconds 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4266 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 96 through 112 Processing helix chain 'A' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 179 through 215 Processing helix chain 'A' and resid 219 through 258 Processing helix chain 'A' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'B' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 96 through 112 Processing helix chain 'B' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 179 through 215 Processing helix chain 'B' and resid 219 through 258 Processing helix chain 'B' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'C' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA C 66 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 96 through 112 Processing helix chain 'C' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 179 through 215 Processing helix chain 'C' and resid 219 through 258 Processing helix chain 'C' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'D' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR D 55 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 96 through 112 Processing helix chain 'D' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 157 through 162 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 179 through 215 Processing helix chain 'D' and resid 219 through 258 Processing helix chain 'D' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'E' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA E 66 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.979A pdb=" N TRP E 80 " --> pdb=" O ASN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 96 through 112 Processing helix chain 'E' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'E' and resid 171 through 177 Processing helix chain 'E' and resid 179 through 215 Processing helix chain 'E' and resid 219 through 258 Processing helix chain 'E' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 306 Processing helix chain 'F' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN F 76 " --> pdb=" O GLY F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 96 through 112 Processing helix chain 'F' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 149 through 154 Processing helix chain 'F' and resid 157 through 162 Processing helix chain 'F' and resid 171 through 177 Processing helix chain 'F' and resid 179 through 215 Processing helix chain 'F' and resid 219 through 258 Processing helix chain 'F' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP F 267 " --> pdb=" O THR F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 306 Processing helix chain 'G' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR G 55 " --> pdb=" O PRO G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 96 through 112 Processing helix chain 'G' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 134 Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 149 through 154 Processing helix chain 'G' and resid 157 through 162 Processing helix chain 'G' and resid 171 through 177 Processing helix chain 'G' and resid 179 through 215 Processing helix chain 'G' and resid 219 through 258 Processing helix chain 'G' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP G 267 " --> pdb=" O THR G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 306 Processing helix chain 'H' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR H 55 " --> pdb=" O PRO H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP H 80 " --> pdb=" O ASN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 96 through 112 Processing helix chain 'H' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 134 Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'H' and resid 149 through 154 Processing helix chain 'H' and resid 157 through 162 Processing helix chain 'H' and resid 171 through 177 Processing helix chain 'H' and resid 179 through 215 Processing helix chain 'H' and resid 219 through 258 Processing helix chain 'H' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP H 267 " --> pdb=" O THR H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 306 Processing helix chain 'I' and resid 51 through 62 removed outlier: 4.021A pdb=" N TYR I 55 " --> pdb=" O PRO I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA I 66 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN I 76 " --> pdb=" O GLY I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 removed outlier: 3.981A pdb=" N TRP I 80 " --> pdb=" O ASN I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 96 through 112 Processing helix chain 'I' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 134 Processing helix chain 'I' and resid 135 through 137 No H-bonds generated for 'chain 'I' and resid 135 through 137' Processing helix chain 'I' and resid 149 through 154 Processing helix chain 'I' and resid 157 through 162 Processing helix chain 'I' and resid 171 through 177 Processing helix chain 'I' and resid 179 through 215 Processing helix chain 'I' and resid 219 through 258 Processing helix chain 'I' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP I 267 " --> pdb=" O THR I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 306 1206 hydrogen bonds defined for protein. 3564 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: 4.78 Time building geometry restraints manager: 7.40 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: 5274 1.34 - 1.45: 3669 1.45 - 1.57: 9228 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 18306 Sorted by residual: bond pdb=" CA PRO I 51 " pdb=" C PRO I 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" CA PRO B 51 " pdb=" C PRO B 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" CA PRO D 51 " pdb=" C PRO D 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" CA PRO G 51 " pdb=" C PRO G 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" CA PRO C 51 " pdb=" C PRO C 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 18301 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.42: 717 107.42 - 114.36: 10323 114.36 - 121.30: 9932 121.30 - 128.24: 3733 128.24 - 135.18: 261 Bond angle restraints: 24966 Sorted by residual: angle pdb=" N SER F 141 " pdb=" CA SER F 141 " pdb=" C SER F 141 " ideal model delta sigma weight residual 114.62 106.09 8.53 1.14e+00 7.69e-01 5.60e+01 angle pdb=" N SER H 141 " pdb=" CA SER H 141 " pdb=" C SER H 141 " ideal model delta sigma weight residual 114.62 106.10 8.52 1.14e+00 7.69e-01 5.59e+01 angle pdb=" N SER C 141 " pdb=" CA SER C 141 " pdb=" C SER C 141 " ideal model delta sigma weight residual 114.62 106.10 8.52 1.14e+00 7.69e-01 5.58e+01 angle pdb=" N SER E 141 " pdb=" CA SER E 141 " pdb=" C SER E 141 " ideal model delta sigma weight residual 114.62 106.11 8.51 1.14e+00 7.69e-01 5.57e+01 angle pdb=" N SER A 141 " pdb=" CA SER A 141 " pdb=" C SER A 141 " ideal model delta sigma weight residual 114.62 106.11 8.51 1.14e+00 7.69e-01 5.57e+01 ... (remaining 24961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9581 17.92 - 35.83: 832 35.83 - 53.75: 171 53.75 - 71.67: 18 71.67 - 89.59: 18 Dihedral angle restraints: 10620 sinusoidal: 4032 harmonic: 6588 Sorted by residual: dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 131 " pdb=" CB CYS C 131 " ideal model delta sinusoidal sigma weight residual 93.00 -177.41 -89.59 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS I 46 " pdb=" SG CYS I 46 " pdb=" SG CYS I 131 " pdb=" CB CYS I 131 " ideal model delta sinusoidal sigma weight residual 93.00 -177.42 -89.58 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS E 46 " pdb=" SG CYS E 46 " pdb=" SG CYS E 131 " pdb=" CB CYS E 131 " ideal model delta sinusoidal sigma weight residual 93.00 -177.42 -89.58 1 1.00e+01 1.00e-02 9.53e+01 ... (remaining 10617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1174 0.032 - 0.065: 997 0.065 - 0.097: 360 0.097 - 0.130: 102 0.130 - 0.162: 103 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CA PRO A 64 " pdb=" N PRO A 64 " pdb=" C PRO A 64 " pdb=" CB PRO A 64 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO H 64 " pdb=" N PRO H 64 " pdb=" C PRO H 64 " pdb=" CB PRO H 64 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA PRO G 64 " pdb=" N PRO G 64 " pdb=" C PRO G 64 " pdb=" CB PRO G 64 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 2733 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 63 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO F 64 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO F 64 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 64 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 63 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO C 64 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 63 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO G 64 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO G 64 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 64 " -0.039 5.00e-02 4.00e+02 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6452 2.85 - 3.37: 17082 3.37 - 3.88: 28066 3.88 - 4.39: 32115 4.39 - 4.90: 55564 Nonbonded interactions: 139279 Sorted by model distance: nonbonded pdb=" O ALA I 143 " pdb=" NZ LYS I 147 " model vdw 2.342 2.520 nonbonded pdb=" O ALA A 143 " pdb=" NZ LYS A 147 " model vdw 2.342 2.520 nonbonded pdb=" O ALA H 143 " pdb=" NZ LYS H 147 " model vdw 2.342 2.520 nonbonded pdb=" O ALA E 143 " pdb=" NZ LYS E 147 " model vdw 2.342 2.520 nonbonded pdb=" O ALA F 143 " pdb=" NZ LYS F 147 " model vdw 2.342 2.520 ... (remaining 139274 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.260 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: 0.020 Extract box with map and model: 2.140 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 46.200 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.009 0.076 18306 Z= 0.553 Angle : 1.002 10.185 24966 Z= 0.597 Chirality : 0.055 0.162 2736 Planarity : 0.008 0.070 3105 Dihedral : 14.135 88.921 6273 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.94 % Allowed : 4.72 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.49 (0.11), residues: 2187 helix: -3.69 (0.07), residues: 1629 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 262 HIS 0.007 0.002 HIS D 56 PHE 0.016 0.002 PHE I 237 TYR 0.027 0.002 TYR E 155 ARG 0.003 0.001 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 448 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 57 SER cc_start: 0.8692 (p) cc_final: 0.8414 (p) REVERT: A 95 HIS cc_start: 0.6952 (m90) cc_final: 0.6689 (m-70) REVERT: A 125 ASP cc_start: 0.8127 (t0) cc_final: 0.7923 (t70) REVERT: A 200 PHE cc_start: 0.7494 (t80) cc_final: 0.7201 (m-10) REVERT: A 236 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8410 (mmmm) REVERT: A 238 ASP cc_start: 0.8462 (m-30) cc_final: 0.8040 (t0) REVERT: A 269 TRP cc_start: 0.7846 (t-100) cc_final: 0.7473 (t-100) REVERT: A 307 LYS cc_start: 0.5497 (mmtt) cc_final: 0.5268 (tmtt) REVERT: B 125 ASP cc_start: 0.8114 (t0) cc_final: 0.7881 (t70) REVERT: B 200 PHE cc_start: 0.7793 (t80) cc_final: 0.7437 (m-10) REVERT: B 227 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8065 (mm-30) REVERT: B 230 LYS cc_start: 0.8189 (mttt) cc_final: 0.7745 (mttm) REVERT: B 235 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 236 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8288 (mmmt) REVERT: B 251 HIS cc_start: 0.7765 (m90) cc_final: 0.7544 (t-90) REVERT: B 260 LYS cc_start: 0.5995 (mmtt) cc_final: 0.5650 (mmtt) REVERT: B 261 ASP cc_start: 0.8226 (t70) cc_final: 0.8000 (t70) REVERT: C 236 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8429 (tppt) REVERT: C 269 TRP cc_start: 0.7761 (t-100) cc_final: 0.7458 (t-100) REVERT: C 297 TYR cc_start: 0.5609 (m-80) cc_final: 0.5251 (m-80) REVERT: D 110 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8135 (tp-100) REVERT: D 222 GLN cc_start: 0.8795 (tt0) cc_final: 0.8466 (tt0) REVERT: D 236 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8307 (tppt) REVERT: D 250 GLU cc_start: 0.7976 (tp30) cc_final: 0.7509 (tm-30) REVERT: E 222 GLN cc_start: 0.8892 (tt0) cc_final: 0.8639 (tt0) REVERT: E 227 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7728 (mm-30) REVERT: E 230 LYS cc_start: 0.8197 (mttt) cc_final: 0.7745 (mtmt) REVERT: E 235 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8354 (tm-30) REVERT: E 236 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8219 (mmmm) REVERT: E 250 GLU cc_start: 0.8026 (tp30) cc_final: 0.7144 (tp30) REVERT: E 269 TRP cc_start: 0.7748 (t-100) cc_final: 0.7533 (t-100) REVERT: E 297 TYR cc_start: 0.5632 (m-80) cc_final: 0.5152 (m-80) REVERT: F 200 PHE cc_start: 0.7944 (t80) cc_final: 0.7391 (m-10) REVERT: F 250 GLU cc_start: 0.7900 (tp30) cc_final: 0.7529 (tm-30) REVERT: F 254 ARG cc_start: 0.8385 (mmt180) cc_final: 0.8012 (mmt-90) REVERT: F 306 ASN cc_start: 0.8354 (m110) cc_final: 0.7921 (p0) REVERT: G 61 MET cc_start: 0.8051 (mtp) cc_final: 0.7706 (mtp) REVERT: G 200 PHE cc_start: 0.7689 (t80) cc_final: 0.7304 (m-10) REVERT: G 222 GLN cc_start: 0.8755 (tt0) cc_final: 0.8444 (tt0) REVERT: G 223 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7835 (tpp-160) REVERT: G 232 VAL cc_start: 0.8693 (t) cc_final: 0.8438 (p) REVERT: G 235 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8159 (tm-30) REVERT: G 250 GLU cc_start: 0.8181 (tp30) cc_final: 0.7619 (tp30) REVERT: G 251 HIS cc_start: 0.7960 (m90) cc_final: 0.7538 (t-170) REVERT: G 269 TRP cc_start: 0.7912 (t-100) cc_final: 0.7696 (t-100) REVERT: G 297 TYR cc_start: 0.5592 (m-80) cc_final: 0.5030 (m-10) REVERT: H 110 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8391 (tp-100) REVERT: H 177 VAL cc_start: 0.8579 (t) cc_final: 0.8292 (p) REVERT: H 200 PHE cc_start: 0.7844 (t80) cc_final: 0.7279 (m-10) REVERT: H 222 GLN cc_start: 0.8875 (tt0) cc_final: 0.8674 (tt0) REVERT: H 227 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7733 (mm-30) REVERT: H 250 GLU cc_start: 0.8195 (tp30) cc_final: 0.7667 (tm-30) REVERT: H 254 ARG cc_start: 0.7862 (mmt180) cc_final: 0.7330 (mmt-90) REVERT: H 269 TRP cc_start: 0.7771 (t-100) cc_final: 0.7545 (t-100) REVERT: I 125 ASP cc_start: 0.8319 (t0) cc_final: 0.8084 (t70) REVERT: I 251 HIS cc_start: 0.7964 (m90) cc_final: 0.7606 (t-170) outliers start: 18 outliers final: 18 residues processed: 466 average time/residue: 0.3998 time to fit residues: 252.7278 Evaluate side-chains 367 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 349 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 176 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 HIS A 110 GLN A 135 HIS A 162 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 135 HIS B 162 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 110 GLN C 135 HIS C 162 ASN C 251 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 110 GLN D 135 HIS D 162 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN E 135 HIS E 162 ASN E 231 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS F 110 GLN F 135 HIS F 162 ASN F 251 HIS ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS G 135 HIS G 162 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS H 110 GLN H 135 HIS H 162 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS I 110 GLN I 135 HIS I 162 ASN I 222 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18306 Z= 0.187 Angle : 0.586 6.862 24966 Z= 0.315 Chirality : 0.038 0.144 2736 Planarity : 0.006 0.060 3105 Dihedral : 6.475 55.467 2421 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.04 % Allowed : 12.95 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.16), residues: 2187 helix: -0.46 (0.11), residues: 1647 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 195 HIS 0.007 0.001 HIS C 251 PHE 0.015 0.001 PHE E 200 TYR 0.008 0.001 TYR I 218 ARG 0.004 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 440 time to evaluate : 2.087 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: A 176 CYS cc_start: 0.5740 (OUTLIER) cc_final: 0.5318 (m) REVERT: A 220 LEU cc_start: 0.7231 (tp) cc_final: 0.7020 (tp) REVERT: A 222 GLN cc_start: 0.8565 (tt0) cc_final: 0.7933 (tt0) REVERT: A 236 LYS cc_start: 0.8458 (mmmt) cc_final: 0.7955 (mmtp) REVERT: A 269 TRP cc_start: 0.7535 (t-100) cc_final: 0.7298 (t-100) REVERT: B 176 CYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5404 (m) REVERT: B 200 PHE cc_start: 0.7900 (t80) cc_final: 0.7207 (m-10) REVERT: B 210 THR cc_start: 0.8162 (m) cc_final: 0.7912 (m) REVERT: B 235 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 236 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8018 (mmtp) REVERT: B 250 GLU cc_start: 0.8082 (tp30) cc_final: 0.7570 (tm-30) REVERT: B 260 LYS cc_start: 0.5582 (mmtt) cc_final: 0.5162 (mmtp) REVERT: C 130 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8050 (ttm170) REVERT: C 136 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7534 (mp0) REVERT: C 176 CYS cc_start: 0.5216 (OUTLIER) cc_final: 0.4737 (m) REVERT: C 213 ARG cc_start: 0.7679 (mmt90) cc_final: 0.7391 (mmt90) REVERT: C 222 GLN cc_start: 0.8729 (tt0) cc_final: 0.8274 (tt0) REVERT: C 250 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7107 (tm-30) REVERT: C 297 TYR cc_start: 0.5587 (m-80) cc_final: 0.5290 (m-10) REVERT: D 48 CYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7431 (m) REVERT: D 82 LEU cc_start: 0.8999 (mt) cc_final: 0.8773 (mt) REVERT: D 110 GLN cc_start: 0.8463 (tp40) cc_final: 0.8109 (tp-100) REVERT: D 176 CYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5802 (m) REVERT: D 199 LEU cc_start: 0.7690 (mp) cc_final: 0.7450 (tp) REVERT: D 222 GLN cc_start: 0.8641 (tt0) cc_final: 0.8291 (tt0) REVERT: D 250 GLU cc_start: 0.8053 (tp30) cc_final: 0.7758 (tp30) REVERT: D 269 TRP cc_start: 0.7296 (t-100) cc_final: 0.7051 (t-100) REVERT: E 176 CYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5542 (m) REVERT: E 230 LYS cc_start: 0.7655 (mttt) cc_final: 0.7442 (mtmt) REVERT: E 235 GLN cc_start: 0.8514 (tm-30) cc_final: 0.7835 (tm-30) REVERT: E 236 LYS cc_start: 0.8301 (mmmt) cc_final: 0.7810 (mmmm) REVERT: E 250 GLU cc_start: 0.7917 (tp30) cc_final: 0.7449 (tp30) REVERT: E 269 TRP cc_start: 0.7572 (t-100) cc_final: 0.7367 (t-100) REVERT: E 297 TYR cc_start: 0.5862 (m-80) cc_final: 0.5402 (m-80) REVERT: F 79 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8738 (p) REVERT: F 176 CYS cc_start: 0.4805 (OUTLIER) cc_final: 0.4098 (m) REVERT: F 213 ARG cc_start: 0.7718 (mmt90) cc_final: 0.7393 (mmt90) REVERT: F 235 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8029 (tm-30) REVERT: F 236 LYS cc_start: 0.8889 (tppt) cc_final: 0.7852 (mmmt) REVERT: F 250 GLU cc_start: 0.7727 (tp30) cc_final: 0.7430 (tp30) REVERT: G 136 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7584 (mt-10) REVERT: G 176 CYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5351 (m) REVERT: G 222 GLN cc_start: 0.8622 (tt0) cc_final: 0.8334 (tt0) REVERT: G 235 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8138 (tm-30) REVERT: G 250 GLU cc_start: 0.7933 (tp30) cc_final: 0.7554 (tp30) REVERT: G 251 HIS cc_start: 0.7782 (m90) cc_final: 0.7535 (t70) REVERT: G 297 TYR cc_start: 0.5600 (m-80) cc_final: 0.5115 (m-10) REVERT: H 110 GLN cc_start: 0.8733 (tp40) cc_final: 0.8426 (tp-100) REVERT: H 136 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7704 (mt-10) REVERT: H 176 CYS cc_start: 0.5529 (OUTLIER) cc_final: 0.5040 (m) REVERT: H 177 VAL cc_start: 0.8462 (t) cc_final: 0.8239 (p) REVERT: I 94 ARG cc_start: 0.8115 (mmt90) cc_final: 0.7826 (mtt90) REVERT: I 176 CYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5104 (m) REVERT: I 222 GLN cc_start: 0.8526 (tt0) cc_final: 0.8171 (tt0) REVERT: I 251 HIS cc_start: 0.7791 (m90) cc_final: 0.7338 (t-90) REVERT: I 269 TRP cc_start: 0.7745 (t-100) cc_final: 0.7365 (t-100) outliers start: 58 outliers final: 32 residues processed: 474 average time/residue: 0.3736 time to fit residues: 245.6927 Evaluate side-chains 394 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 351 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 266 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 194 optimal weight: 0.0010 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN E 110 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** F 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18306 Z= 0.148 Angle : 0.514 5.990 24966 Z= 0.272 Chirality : 0.037 0.143 2736 Planarity : 0.005 0.046 3105 Dihedral : 5.635 59.218 2413 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.61 % Allowed : 13.73 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2187 helix: 1.37 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -2.05 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 195 HIS 0.002 0.001 HIS G 56 PHE 0.018 0.001 PHE H 200 TYR 0.010 0.001 TYR H 218 ARG 0.006 0.001 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 391 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 CYS cc_start: 0.5882 (OUTLIER) cc_final: 0.5275 (m) REVERT: A 269 TRP cc_start: 0.7721 (t-100) cc_final: 0.7426 (t-100) REVERT: B 89 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6276 (ttt-90) REVERT: B 95 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.6167 (m90) REVERT: B 176 CYS cc_start: 0.6418 (OUTLIER) cc_final: 0.5708 (m) REVERT: B 200 PHE cc_start: 0.7860 (t80) cc_final: 0.7139 (m-10) REVERT: B 222 GLN cc_start: 0.8863 (tt0) cc_final: 0.8458 (tt0) REVERT: B 235 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8472 (tm-30) REVERT: B 236 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7959 (mmtm) REVERT: B 250 GLU cc_start: 0.7821 (tp30) cc_final: 0.7545 (tp30) REVERT: B 260 LYS cc_start: 0.5419 (mmtt) cc_final: 0.5100 (mmtp) REVERT: C 130 ARG cc_start: 0.8369 (ttm170) cc_final: 0.7945 (ttm170) REVERT: C 136 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7924 (mt-10) REVERT: C 176 CYS cc_start: 0.5761 (OUTLIER) cc_final: 0.5229 (m) REVERT: C 222 GLN cc_start: 0.8682 (tt0) cc_final: 0.8231 (tt0) REVERT: C 236 LYS cc_start: 0.8496 (mmmt) cc_final: 0.7839 (mmmt) REVERT: C 250 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6764 (tm-30) REVERT: C 265 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7071 (ttt90) REVERT: D 94 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7528 (mtt90) REVERT: D 110 GLN cc_start: 0.8494 (tp40) cc_final: 0.8137 (tp-100) REVERT: D 144 ILE cc_start: 0.8222 (mp) cc_final: 0.7928 (mt) REVERT: D 176 CYS cc_start: 0.5816 (OUTLIER) cc_final: 0.5316 (m) REVERT: D 222 GLN cc_start: 0.8609 (tt0) cc_final: 0.8261 (tt0) REVERT: E 176 CYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5645 (m) REVERT: E 222 GLN cc_start: 0.8777 (tt0) cc_final: 0.8542 (tt0) REVERT: E 235 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8325 (tm-30) REVERT: E 236 LYS cc_start: 0.8303 (mmmt) cc_final: 0.8030 (mmmm) REVERT: E 250 GLU cc_start: 0.7770 (tp30) cc_final: 0.7476 (tp30) REVERT: E 297 TYR cc_start: 0.5912 (m-80) cc_final: 0.5614 (m-10) REVERT: F 176 CYS cc_start: 0.5370 (OUTLIER) cc_final: 0.4733 (m) REVERT: F 222 GLN cc_start: 0.8700 (tt0) cc_final: 0.8341 (tt0) REVERT: F 235 GLN cc_start: 0.8624 (tm-30) cc_final: 0.7992 (tm-30) REVERT: F 236 LYS cc_start: 0.8849 (tppt) cc_final: 0.7951 (mmmt) REVERT: F 238 ASP cc_start: 0.8197 (m-30) cc_final: 0.7963 (m-30) REVERT: F 254 ARG cc_start: 0.8000 (mmt-90) cc_final: 0.7669 (mmt-90) REVERT: F 269 TRP cc_start: 0.7839 (t-100) cc_final: 0.7557 (t-100) REVERT: G 136 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7681 (mt-10) REVERT: G 176 CYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5475 (m) REVERT: G 222 GLN cc_start: 0.8766 (tt0) cc_final: 0.8463 (tt0) REVERT: G 235 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8093 (tm-30) REVERT: G 250 GLU cc_start: 0.7901 (tp30) cc_final: 0.7494 (tm-30) REVERT: G 254 ARG cc_start: 0.7905 (tpp80) cc_final: 0.7692 (tpp80) REVERT: G 269 TRP cc_start: 0.8016 (t-100) cc_final: 0.7706 (t-100) REVERT: H 89 ARG cc_start: 0.6997 (ttt180) cc_final: 0.6778 (ttt180) REVERT: H 97 TRP cc_start: 0.6418 (p-90) cc_final: 0.6135 (m-10) REVERT: H 110 GLN cc_start: 0.8758 (tp40) cc_final: 0.8467 (tp-100) REVERT: H 163 LYS cc_start: 0.7320 (ttmt) cc_final: 0.7095 (ttmt) REVERT: H 176 CYS cc_start: 0.5820 (OUTLIER) cc_final: 0.5396 (m) REVERT: H 254 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.7513 (mmt-90) REVERT: I 97 TRP cc_start: 0.5964 (m-10) cc_final: 0.5755 (m-10) REVERT: I 176 CYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5597 (m) REVERT: I 269 TRP cc_start: 0.7626 (t-100) cc_final: 0.7384 (t-100) outliers start: 88 outliers final: 50 residues processed: 447 average time/residue: 0.3676 time to fit residues: 227.5552 Evaluate side-chains 394 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 332 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 214 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN A 224 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18306 Z= 0.232 Angle : 0.558 8.635 24966 Z= 0.292 Chirality : 0.040 0.139 2736 Planarity : 0.005 0.050 3105 Dihedral : 5.591 59.828 2412 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.82 % Allowed : 16.46 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.18), residues: 2187 helix: 2.03 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.88 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 267 HIS 0.005 0.001 HIS G 251 PHE 0.011 0.001 PHE H 200 TYR 0.010 0.001 TYR H 218 ARG 0.010 0.001 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 352 time to evaluate : 2.242 Fit side-chains revert: symmetry clash REVERT: A 176 CYS cc_start: 0.6064 (OUTLIER) cc_final: 0.5552 (m) REVERT: A 222 GLN cc_start: 0.8540 (tt0) cc_final: 0.8041 (tt0) REVERT: A 235 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 269 TRP cc_start: 0.7755 (t-100) cc_final: 0.7442 (t-100) REVERT: B 92 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6787 (p0) REVERT: B 95 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6880 (m90) REVERT: B 176 CYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5539 (m) REVERT: B 200 PHE cc_start: 0.7841 (t80) cc_final: 0.7152 (m-10) REVERT: B 222 GLN cc_start: 0.8934 (tt0) cc_final: 0.8502 (tt0) REVERT: B 235 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8450 (tm-30) REVERT: B 250 GLU cc_start: 0.7830 (tp30) cc_final: 0.7568 (tm-30) REVERT: B 260 LYS cc_start: 0.5423 (mmtt) cc_final: 0.5102 (mmtp) REVERT: C 91 ARG cc_start: 0.6919 (tpp-160) cc_final: 0.6230 (tpp-160) REVERT: C 130 ARG cc_start: 0.8401 (ttm170) cc_final: 0.7974 (ttm170) REVERT: C 176 CYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5354 (m) REVERT: C 222 GLN cc_start: 0.8672 (tt0) cc_final: 0.8161 (tt0) REVERT: D 94 ARG cc_start: 0.7925 (mmt90) cc_final: 0.7592 (mtt90) REVERT: D 110 GLN cc_start: 0.8489 (tp40) cc_final: 0.8131 (tp-100) REVERT: D 144 ILE cc_start: 0.8204 (mp) cc_final: 0.7914 (mt) REVERT: D 176 CYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5519 (m) REVERT: D 222 GLN cc_start: 0.8684 (tt0) cc_final: 0.8308 (tt0) REVERT: E 176 CYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5447 (m) REVERT: E 222 GLN cc_start: 0.8816 (tt0) cc_final: 0.8569 (tt0) REVERT: E 235 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8189 (tm-30) REVERT: E 236 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7645 (mmtm) REVERT: E 297 TYR cc_start: 0.5933 (m-80) cc_final: 0.5643 (m-10) REVERT: F 58 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7917 (mt) REVERT: F 133 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8035 (ttt90) REVERT: F 176 CYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5415 (m) REVERT: F 222 GLN cc_start: 0.8732 (tt0) cc_final: 0.8284 (tt0) REVERT: F 236 LYS cc_start: 0.8884 (tppt) cc_final: 0.8239 (mmmt) REVERT: F 250 GLU cc_start: 0.7885 (tp30) cc_final: 0.7059 (tp30) REVERT: G 136 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7589 (mt-10) REVERT: G 176 CYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5166 (m) REVERT: G 222 GLN cc_start: 0.8811 (tt0) cc_final: 0.8506 (tt0) REVERT: G 251 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.7070 (t-90) REVERT: H 89 ARG cc_start: 0.7143 (ttt180) cc_final: 0.6855 (ttt180) REVERT: H 123 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8432 (m-10) REVERT: H 136 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7521 (mt-10) REVERT: H 176 CYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5381 (m) REVERT: H 265 ARG cc_start: 0.7847 (ttt180) cc_final: 0.7527 (ttt-90) REVERT: I 97 TRP cc_start: 0.6020 (OUTLIER) cc_final: 0.5744 (m-10) REVERT: I 176 CYS cc_start: 0.5978 (OUTLIER) cc_final: 0.5398 (m) REVERT: I 222 GLN cc_start: 0.8512 (tt0) cc_final: 0.8026 (tt0) REVERT: I 269 TRP cc_start: 0.7635 (t-100) cc_final: 0.7385 (t-100) outliers start: 111 outliers final: 78 residues processed: 422 average time/residue: 0.3874 time to fit residues: 229.2320 Evaluate side-chains 417 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 324 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 PHE Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 3 optimal weight: 0.0970 chunk 155 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18306 Z= 0.140 Angle : 0.494 7.656 24966 Z= 0.261 Chirality : 0.037 0.149 2736 Planarity : 0.004 0.046 3105 Dihedral : 5.428 59.856 2412 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.93 % Allowed : 17.98 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.18), residues: 2187 helix: 2.57 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.94 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 269 HIS 0.029 0.001 HIS G 251 PHE 0.010 0.001 PHE B 256 TYR 0.008 0.001 TYR I 128 ARG 0.009 0.001 ARG I 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 345 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 CYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5303 (m) REVERT: A 191 GLN cc_start: 0.7901 (mt0) cc_final: 0.7591 (mp10) REVERT: A 269 TRP cc_start: 0.7745 (t-100) cc_final: 0.7421 (t-100) REVERT: B 136 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7733 (pt0) REVERT: B 176 CYS cc_start: 0.6422 (OUTLIER) cc_final: 0.5643 (m) REVERT: B 200 PHE cc_start: 0.7850 (t80) cc_final: 0.7139 (m-10) REVERT: B 235 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8485 (tm-30) REVERT: B 250 GLU cc_start: 0.7716 (tp30) cc_final: 0.7464 (tm-30) REVERT: B 260 LYS cc_start: 0.5502 (mmtt) cc_final: 0.5185 (mmtp) REVERT: C 130 ARG cc_start: 0.8366 (ttm170) cc_final: 0.8009 (ttm170) REVERT: C 176 CYS cc_start: 0.5894 (OUTLIER) cc_final: 0.5307 (m) REVERT: C 222 GLN cc_start: 0.8691 (tt0) cc_final: 0.8210 (tt0) REVERT: C 235 GLN cc_start: 0.8281 (tm-30) cc_final: 0.8035 (tm-30) REVERT: C 250 GLU cc_start: 0.7968 (tp30) cc_final: 0.7326 (tp30) REVERT: D 94 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7600 (mtt90) REVERT: D 110 GLN cc_start: 0.8438 (tp40) cc_final: 0.8050 (tp-100) REVERT: D 144 ILE cc_start: 0.8191 (mp) cc_final: 0.7813 (mt) REVERT: D 176 CYS cc_start: 0.5731 (OUTLIER) cc_final: 0.5296 (m) REVERT: D 222 GLN cc_start: 0.8624 (tt0) cc_final: 0.8248 (tt0) REVERT: D 269 TRP cc_start: 0.7587 (t-100) cc_final: 0.7142 (t-100) REVERT: E 176 CYS cc_start: 0.5997 (OUTLIER) cc_final: 0.5379 (m) REVERT: E 222 GLN cc_start: 0.8785 (tt0) cc_final: 0.8545 (tt0) REVERT: E 235 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8196 (tm-30) REVERT: E 236 LYS cc_start: 0.8346 (mmmt) cc_final: 0.8102 (mmmm) REVERT: F 176 CYS cc_start: 0.5668 (OUTLIER) cc_final: 0.5058 (m) REVERT: F 235 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8365 (tm-30) REVERT: F 250 GLU cc_start: 0.7686 (tp30) cc_final: 0.7372 (tp30) REVERT: G 176 CYS cc_start: 0.5873 (OUTLIER) cc_final: 0.5138 (m) REVERT: G 222 GLN cc_start: 0.8772 (tt0) cc_final: 0.8493 (tt0) REVERT: G 251 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.6849 (t-170) REVERT: G 269 TRP cc_start: 0.8309 (t-100) cc_final: 0.7955 (t-100) REVERT: H 89 ARG cc_start: 0.7083 (ttt180) cc_final: 0.6574 (ttt180) REVERT: H 176 CYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5350 (m) REVERT: I 176 CYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5331 (m) REVERT: I 218 TYR cc_start: 0.8557 (m-10) cc_final: 0.8354 (m-10) REVERT: I 235 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8347 (tm-30) outliers start: 94 outliers final: 60 residues processed: 409 average time/residue: 0.3841 time to fit residues: 222.1232 Evaluate side-chains 393 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 323 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 155 TYR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18306 Z= 0.165 Angle : 0.504 8.067 24966 Z= 0.264 Chirality : 0.038 0.139 2736 Planarity : 0.004 0.045 3105 Dihedral : 5.375 59.967 2412 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.35 % Allowed : 18.66 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.18), residues: 2187 helix: 2.77 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.92 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 267 HIS 0.015 0.001 HIS G 251 PHE 0.014 0.001 PHE A 200 TYR 0.014 0.001 TYR A 218 ARG 0.008 0.001 ARG I 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 334 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.6893 (m90) cc_final: 0.6672 (m90) REVERT: A 176 CYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5523 (m) REVERT: A 222 GLN cc_start: 0.8352 (tt0) cc_final: 0.7784 (tt0) REVERT: A 235 GLN cc_start: 0.8838 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 269 TRP cc_start: 0.7741 (t-100) cc_final: 0.7422 (t-100) REVERT: B 91 ARG cc_start: 0.7004 (tpp-160) cc_final: 0.6485 (tpm170) REVERT: B 95 HIS cc_start: 0.7119 (OUTLIER) cc_final: 0.6853 (m90) REVERT: B 136 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7687 (pt0) REVERT: B 176 CYS cc_start: 0.6218 (OUTLIER) cc_final: 0.5434 (m) REVERT: B 200 PHE cc_start: 0.7845 (t80) cc_final: 0.7141 (m-10) REVERT: B 235 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8502 (tm-30) REVERT: B 250 GLU cc_start: 0.7674 (tp30) cc_final: 0.7434 (tm-30) REVERT: B 260 LYS cc_start: 0.5468 (mmtt) cc_final: 0.5160 (mmtp) REVERT: C 98 LYS cc_start: 0.5922 (tptt) cc_final: 0.5419 (pptt) REVERT: C 130 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8051 (ttm170) REVERT: C 176 CYS cc_start: 0.5943 (OUTLIER) cc_final: 0.5337 (m) REVERT: C 222 GLN cc_start: 0.8698 (tt0) cc_final: 0.8215 (tt0) REVERT: C 250 GLU cc_start: 0.8025 (tp30) cc_final: 0.7392 (tp30) REVERT: D 94 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7567 (mtt90) REVERT: D 110 GLN cc_start: 0.8416 (tp40) cc_final: 0.8057 (tp-100) REVERT: D 144 ILE cc_start: 0.8173 (mp) cc_final: 0.7785 (mt) REVERT: D 176 CYS cc_start: 0.5677 (OUTLIER) cc_final: 0.5259 (m) REVERT: D 222 GLN cc_start: 0.8619 (tt0) cc_final: 0.8257 (tt0) REVERT: D 265 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7747 (ttt-90) REVERT: D 269 TRP cc_start: 0.7527 (t-100) cc_final: 0.7113 (t-100) REVERT: E 176 CYS cc_start: 0.6096 (OUTLIER) cc_final: 0.5459 (m) REVERT: E 222 GLN cc_start: 0.8799 (tt0) cc_final: 0.8543 (tt0) REVERT: E 235 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8188 (tm-30) REVERT: E 236 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7966 (mmmm) REVERT: E 247 GLN cc_start: 0.7853 (mt0) cc_final: 0.7505 (mt0) REVERT: F 176 CYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5560 (m) REVERT: F 250 GLU cc_start: 0.7714 (tp30) cc_final: 0.7213 (tp30) REVERT: G 163 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7411 (ttmt) REVERT: G 176 CYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5161 (m) REVERT: G 222 GLN cc_start: 0.8780 (tt0) cc_final: 0.8257 (tt0) REVERT: G 269 TRP cc_start: 0.8308 (t-100) cc_final: 0.7991 (t-100) REVERT: H 89 ARG cc_start: 0.7079 (ttt180) cc_final: 0.6823 (ttt180) REVERT: H 176 CYS cc_start: 0.5854 (OUTLIER) cc_final: 0.5347 (m) REVERT: I 94 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7323 (mtt90) REVERT: I 176 CYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5388 (m) REVERT: I 235 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8309 (tm-30) outliers start: 102 outliers final: 77 residues processed: 401 average time/residue: 0.3461 time to fit residues: 197.4426 Evaluate side-chains 408 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 321 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 238 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 4.9990 chunk 23 optimal weight: 0.0970 chunk 119 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN E 251 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18306 Z= 0.146 Angle : 0.489 7.427 24966 Z= 0.257 Chirality : 0.037 0.139 2736 Planarity : 0.004 0.046 3105 Dihedral : 5.313 59.482 2412 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.98 % Allowed : 19.34 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.18), residues: 2187 helix: 2.93 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.89 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 267 HIS 0.022 0.001 HIS E 251 PHE 0.010 0.001 PHE D 44 TYR 0.010 0.001 TYR A 218 ARG 0.010 0.001 ARG I 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 329 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.6909 (m90) cc_final: 0.6697 (m90) REVERT: A 176 CYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5479 (m) REVERT: A 191 GLN cc_start: 0.7905 (mt0) cc_final: 0.7596 (mp10) REVERT: A 269 TRP cc_start: 0.7597 (t-100) cc_final: 0.7334 (t-100) REVERT: B 89 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6485 (ttt-90) REVERT: B 95 HIS cc_start: 0.7053 (OUTLIER) cc_final: 0.6280 (m90) REVERT: B 136 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7807 (pt0) REVERT: B 176 CYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5428 (m) REVERT: B 200 PHE cc_start: 0.7855 (t80) cc_final: 0.7147 (m-10) REVERT: B 235 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8529 (tm-30) REVERT: B 250 GLU cc_start: 0.7641 (tp30) cc_final: 0.7394 (tm-30) REVERT: B 260 LYS cc_start: 0.5458 (mmtt) cc_final: 0.5115 (mttm) REVERT: C 98 LYS cc_start: 0.5912 (tptt) cc_final: 0.5410 (pptt) REVERT: C 176 CYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5334 (m) REVERT: C 222 GLN cc_start: 0.8685 (tt0) cc_final: 0.8212 (tt0) REVERT: C 250 GLU cc_start: 0.8036 (tp30) cc_final: 0.7416 (tp30) REVERT: D 94 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7574 (mtt90) REVERT: D 110 GLN cc_start: 0.8433 (tp40) cc_final: 0.8038 (tp-100) REVERT: D 176 CYS cc_start: 0.5688 (OUTLIER) cc_final: 0.5264 (m) REVERT: D 222 GLN cc_start: 0.8616 (tt0) cc_final: 0.8245 (tt0) REVERT: D 269 TRP cc_start: 0.7521 (t-100) cc_final: 0.7172 (t-100) REVERT: E 136 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7695 (pt0) REVERT: E 176 CYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5434 (m) REVERT: E 235 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8184 (tm-30) REVERT: E 236 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7935 (mmmm) REVERT: E 247 GLN cc_start: 0.7762 (mt0) cc_final: 0.7462 (mt0) REVERT: F 97 TRP cc_start: 0.6417 (p-90) cc_final: 0.5913 (m-10) REVERT: F 176 CYS cc_start: 0.6159 (OUTLIER) cc_final: 0.5556 (m) REVERT: G 176 CYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5155 (m) REVERT: G 222 GLN cc_start: 0.8771 (tt0) cc_final: 0.8288 (tt0) REVERT: G 250 GLU cc_start: 0.7654 (tp30) cc_final: 0.6929 (tt0) REVERT: G 269 TRP cc_start: 0.8278 (t-100) cc_final: 0.7994 (t-100) REVERT: H 89 ARG cc_start: 0.6969 (ttt180) cc_final: 0.6393 (ttt180) REVERT: H 176 CYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5309 (m) REVERT: I 176 CYS cc_start: 0.5978 (OUTLIER) cc_final: 0.5383 (m) REVERT: I 232 VAL cc_start: 0.8766 (t) cc_final: 0.8506 (p) REVERT: I 235 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8302 (tm-30) outliers start: 95 outliers final: 76 residues processed: 392 average time/residue: 0.3555 time to fit residues: 197.4382 Evaluate side-chains 401 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 314 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 155 TYR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 238 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18306 Z= 0.165 Angle : 0.499 6.967 24966 Z= 0.261 Chirality : 0.038 0.138 2736 Planarity : 0.004 0.045 3105 Dihedral : 5.277 58.855 2412 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.93 % Allowed : 19.86 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.18), residues: 2187 helix: 2.98 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.83 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 269 HIS 0.004 0.001 HIS A 56 PHE 0.010 0.001 PHE D 200 TYR 0.010 0.001 TYR C 229 ARG 0.009 0.001 ARG I 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 329 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.6653 (m90) cc_final: 0.6394 (m90) REVERT: A 176 CYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5520 (m) REVERT: A 235 GLN cc_start: 0.8828 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 89 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6469 (ttt-90) REVERT: B 95 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.6490 (m90) REVERT: B 136 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7791 (pt0) REVERT: B 176 CYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5356 (m) REVERT: B 200 PHE cc_start: 0.7846 (t80) cc_final: 0.7138 (m-10) REVERT: B 235 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8506 (tm-30) REVERT: B 250 GLU cc_start: 0.7685 (tp30) cc_final: 0.7431 (tm-30) REVERT: B 260 LYS cc_start: 0.5521 (mmtt) cc_final: 0.5179 (mttm) REVERT: C 98 LYS cc_start: 0.5919 (tptt) cc_final: 0.5417 (pptt) REVERT: C 176 CYS cc_start: 0.5978 (OUTLIER) cc_final: 0.5356 (m) REVERT: C 222 GLN cc_start: 0.8697 (tt0) cc_final: 0.8211 (tt0) REVERT: D 94 ARG cc_start: 0.8051 (mmt90) cc_final: 0.7691 (mtt90) REVERT: D 110 GLN cc_start: 0.8436 (tp40) cc_final: 0.8028 (tp-100) REVERT: D 176 CYS cc_start: 0.5715 (OUTLIER) cc_final: 0.5277 (m) REVERT: D 222 GLN cc_start: 0.8631 (tt0) cc_final: 0.8231 (tt0) REVERT: E 136 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7668 (pt0) REVERT: E 176 CYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5615 (m) REVERT: E 235 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8097 (tm-30) REVERT: E 236 LYS cc_start: 0.8264 (mmmt) cc_final: 0.7706 (mmtm) REVERT: E 247 GLN cc_start: 0.7810 (mt0) cc_final: 0.7523 (mt0) REVERT: F 97 TRP cc_start: 0.6399 (p-90) cc_final: 0.5903 (m-10) REVERT: F 176 CYS cc_start: 0.6345 (OUTLIER) cc_final: 0.5651 (m) REVERT: G 163 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7430 (ttmt) REVERT: G 176 CYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5188 (m) REVERT: G 222 GLN cc_start: 0.8772 (tt0) cc_final: 0.8287 (tt0) REVERT: G 250 GLU cc_start: 0.7813 (tp30) cc_final: 0.7095 (tt0) REVERT: G 269 TRP cc_start: 0.8284 (t-100) cc_final: 0.8019 (t-100) REVERT: H 163 LYS cc_start: 0.7411 (ttmt) cc_final: 0.7038 (ttmt) REVERT: H 176 CYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5410 (m) REVERT: I 91 ARG cc_start: 0.7410 (mmt90) cc_final: 0.7142 (tpt170) REVERT: I 176 CYS cc_start: 0.6020 (OUTLIER) cc_final: 0.5416 (m) REVERT: I 232 VAL cc_start: 0.8775 (t) cc_final: 0.8517 (p) REVERT: I 235 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8311 (tm-30) outliers start: 94 outliers final: 78 residues processed: 390 average time/residue: 0.3534 time to fit residues: 194.8450 Evaluate side-chains 407 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 318 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 155 TYR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 238 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 194 optimal weight: 0.1980 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 175 optimal weight: 0.0470 chunk 183 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 chunk 127 optimal weight: 0.0970 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18306 Z= 0.130 Angle : 0.486 8.596 24966 Z= 0.255 Chirality : 0.037 0.138 2736 Planarity : 0.004 0.047 3105 Dihedral : 5.200 59.282 2412 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.30 % Allowed : 20.18 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.18), residues: 2187 helix: 3.18 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.87 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 269 HIS 0.002 0.000 HIS B 56 PHE 0.012 0.001 PHE D 200 TYR 0.011 0.001 TYR I 218 ARG 0.010 0.001 ARG I 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 324 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 CYS cc_start: 0.6018 (OUTLIER) cc_final: 0.5497 (m) REVERT: A 191 GLN cc_start: 0.7896 (mt0) cc_final: 0.7692 (mp10) REVERT: A 235 GLN cc_start: 0.8810 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 247 GLN cc_start: 0.8035 (mt0) cc_final: 0.7744 (mt0) REVERT: A 297 TYR cc_start: 0.5848 (m-80) cc_final: 0.5553 (m-80) REVERT: B 89 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6406 (ttt-90) REVERT: B 95 HIS cc_start: 0.6948 (OUTLIER) cc_final: 0.6292 (m90) REVERT: B 176 CYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5436 (m) REVERT: B 200 PHE cc_start: 0.7853 (t80) cc_final: 0.7139 (m-10) REVERT: B 235 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8593 (tm-30) REVERT: B 250 GLU cc_start: 0.7621 (tp30) cc_final: 0.7362 (tm-30) REVERT: B 301 GLN cc_start: 0.7307 (mt0) cc_final: 0.7020 (mt0) REVERT: C 98 LYS cc_start: 0.5898 (tptt) cc_final: 0.5404 (pptt) REVERT: C 176 CYS cc_start: 0.5919 (OUTLIER) cc_final: 0.5310 (m) REVERT: C 222 GLN cc_start: 0.8700 (tt0) cc_final: 0.8206 (tt0) REVERT: C 235 GLN cc_start: 0.8248 (tm-30) cc_final: 0.8030 (tm-30) REVERT: D 94 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7623 (mtt90) REVERT: D 110 GLN cc_start: 0.8415 (tp40) cc_final: 0.7965 (tp-100) REVERT: D 176 CYS cc_start: 0.5691 (OUTLIER) cc_final: 0.5269 (m) REVERT: D 222 GLN cc_start: 0.8597 (tt0) cc_final: 0.8208 (tt0) REVERT: E 176 CYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5433 (m) REVERT: E 222 GLN cc_start: 0.8759 (tt0) cc_final: 0.8223 (tt0) REVERT: E 235 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8127 (tm-30) REVERT: E 236 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7603 (mmtm) REVERT: E 247 GLN cc_start: 0.7786 (mt0) cc_final: 0.7465 (mt0) REVERT: F 97 TRP cc_start: 0.6562 (p-90) cc_final: 0.5997 (m-10) REVERT: F 176 CYS cc_start: 0.6137 (OUTLIER) cc_final: 0.5522 (m) REVERT: F 250 GLU cc_start: 0.7657 (tp30) cc_final: 0.6910 (tm-30) REVERT: F 254 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7866 (tpp80) REVERT: G 176 CYS cc_start: 0.6054 (OUTLIER) cc_final: 0.5353 (m) REVERT: G 250 GLU cc_start: 0.7661 (tp30) cc_final: 0.6915 (tt0) REVERT: G 269 TRP cc_start: 0.8250 (t-100) cc_final: 0.7982 (t-100) REVERT: H 176 CYS cc_start: 0.5838 (OUTLIER) cc_final: 0.5338 (m) REVERT: I 136 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7647 (pt0) REVERT: I 176 CYS cc_start: 0.5974 (OUTLIER) cc_final: 0.5370 (m) REVERT: I 232 VAL cc_start: 0.8816 (t) cc_final: 0.8566 (p) REVERT: I 235 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8332 (tm-30) REVERT: I 247 GLN cc_start: 0.8356 (tt0) cc_final: 0.7974 (mt0) outliers start: 82 outliers final: 60 residues processed: 382 average time/residue: 0.3597 time to fit residues: 195.7236 Evaluate side-chains 381 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 310 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 142 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18306 Z= 0.174 Angle : 0.515 8.930 24966 Z= 0.268 Chirality : 0.038 0.138 2736 Planarity : 0.004 0.046 3105 Dihedral : 5.215 59.171 2412 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.25 % Allowed : 20.70 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.18), residues: 2187 helix: 3.08 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.81 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 269 HIS 0.005 0.001 HIS A 56 PHE 0.013 0.001 PHE D 200 TYR 0.008 0.001 TYR B 185 ARG 0.009 0.001 ARG I 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 312 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 CYS cc_start: 0.6062 (OUTLIER) cc_final: 0.5525 (m) REVERT: A 191 GLN cc_start: 0.7995 (mt0) cc_final: 0.7637 (mp10) REVERT: A 235 GLN cc_start: 0.8831 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 247 GLN cc_start: 0.7964 (mt0) cc_final: 0.7658 (mt0) REVERT: B 89 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6479 (ttt-90) REVERT: B 91 ARG cc_start: 0.6987 (tpp-160) cc_final: 0.6490 (tpm170) REVERT: B 95 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6378 (m90) REVERT: B 176 CYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5369 (m) REVERT: B 200 PHE cc_start: 0.7853 (t80) cc_final: 0.7150 (m-10) REVERT: B 235 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8520 (tm-30) REVERT: B 250 GLU cc_start: 0.7580 (tp30) cc_final: 0.7353 (tm-30) REVERT: B 301 GLN cc_start: 0.7394 (mt0) cc_final: 0.7107 (mt0) REVERT: C 130 ARG cc_start: 0.8372 (ttm170) cc_final: 0.8100 (ttm170) REVERT: C 176 CYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5347 (m) REVERT: C 222 GLN cc_start: 0.8684 (tt0) cc_final: 0.8201 (tt0) REVERT: C 235 GLN cc_start: 0.8232 (tm-30) cc_final: 0.8006 (tm-30) REVERT: D 61 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7620 (mtp) REVERT: D 94 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7724 (mtt90) REVERT: D 110 GLN cc_start: 0.8436 (tp40) cc_final: 0.8010 (tp-100) REVERT: D 176 CYS cc_start: 0.5751 (OUTLIER) cc_final: 0.5308 (m) REVERT: D 222 GLN cc_start: 0.8620 (tt0) cc_final: 0.8233 (tt0) REVERT: E 136 GLU cc_start: 0.7817 (pt0) cc_final: 0.7611 (pt0) REVERT: E 176 CYS cc_start: 0.6125 (OUTLIER) cc_final: 0.5624 (m) REVERT: E 222 GLN cc_start: 0.8780 (tt0) cc_final: 0.8202 (tt0) REVERT: E 235 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8136 (tm-30) REVERT: E 236 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7619 (mmtm) REVERT: E 247 GLN cc_start: 0.7798 (mt0) cc_final: 0.7482 (mt0) REVERT: F 97 TRP cc_start: 0.6585 (p-90) cc_final: 0.6018 (m-10) REVERT: F 133 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7653 (ttm-80) REVERT: F 176 CYS cc_start: 0.6352 (OUTLIER) cc_final: 0.5654 (m) REVERT: F 250 GLU cc_start: 0.7700 (tp30) cc_final: 0.7437 (tm-30) REVERT: G 163 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7431 (ttmt) REVERT: G 176 CYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5206 (m) REVERT: G 222 GLN cc_start: 0.8782 (tt0) cc_final: 0.8226 (tt0) REVERT: G 250 GLU cc_start: 0.7872 (tp30) cc_final: 0.7141 (tt0) REVERT: G 269 TRP cc_start: 0.8258 (t-100) cc_final: 0.8009 (t-100) REVERT: H 176 CYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5760 (m) REVERT: I 176 CYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5470 (m) REVERT: I 232 VAL cc_start: 0.8779 (t) cc_final: 0.8533 (p) REVERT: I 235 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8351 (tm-30) REVERT: I 247 GLN cc_start: 0.8352 (tt0) cc_final: 0.7972 (mt0) outliers start: 81 outliers final: 68 residues processed: 367 average time/residue: 0.3506 time to fit residues: 181.7501 Evaluate side-chains 386 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 306 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 155 TYR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 306 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.0050 chunk 150 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115937 restraints weight = 25606.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119175 restraints weight = 14518.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121226 restraints weight = 10502.566| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18306 Z= 0.142 Angle : 0.497 8.973 24966 Z= 0.260 Chirality : 0.037 0.139 2736 Planarity : 0.004 0.047 3105 Dihedral : 5.189 59.141 2412 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.45 % Allowed : 20.60 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.18), residues: 2187 helix: 3.15 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.79 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 267 HIS 0.002 0.001 HIS B 56 PHE 0.011 0.001 PHE D 200 TYR 0.007 0.001 TYR C 229 ARG 0.010 0.001 ARG I 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4037.05 seconds wall clock time: 74 minutes 3.22 seconds (4443.22 seconds total)