Starting phenix.real_space_refine on Wed Mar 20 19:07:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/03_2024/7ock_12809.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/03_2024/7ock_12809.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/7ock_12809/03_2024/7ock_12809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/03_2024/7ock_12809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/03_2024/7ock_12809.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/03_2024/7ock_12809.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= 0.042 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 136 5.16 5 C 17822 2.51 5 N 4884 2.21 5 O 5434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 334": "OD1" <-> "OD2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 101": "OD1" <-> "OD2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C ASP 174": "OD1" <-> "OD2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 249": "OD1" <-> "OD2" Residue "C ASP 266": "OD1" <-> "OD2" Residue "C ASP 271": "OD1" <-> "OD2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 334": "OD1" <-> "OD2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C ASP 378": "OD1" <-> "OD2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "D ASP 131": "OD1" <-> "OD2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 238": "OD1" <-> "OD2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D ASP 266": "OD1" <-> "OD2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D ASP 334": "OD1" <-> "OD2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "E ASP 20": "OD1" <-> "OD2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "E ASP 118": "OD1" <-> "OD2" Residue "E ASP 131": "OD1" <-> "OD2" Residue "E ASP 173": "OD1" <-> "OD2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 266": "OD1" <-> "OD2" Residue "E ASP 271": "OD1" <-> "OD2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E GLU 295": "OE1" <-> "OE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 331": "OE1" <-> "OE2" Residue "E PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E GLU 368": "OE1" <-> "OE2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F GLU 65": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 118": "OD1" <-> "OD2" Residue "F ASP 131": "OD1" <-> "OD2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ASP 173": "OD1" <-> "OD2" Residue "F ASP 174": "OD1" <-> "OD2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F GLU 323": "OE1" <-> "OE2" Residue "F GLU 331": "OE1" <-> "OE2" Residue "F PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 334": "OD1" <-> "OD2" Residue "F TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G ASP 20": "OD1" <-> "OD2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 107": "OD1" <-> "OD2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 173": "OD1" <-> "OD2" Residue "G ASP 174": "OD1" <-> "OD2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G ASP 249": "OD1" <-> "OD2" Residue "G PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 331": "OE1" <-> "OE2" Residue "G PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 334": "OD1" <-> "OD2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "G GLU 368": "OE1" <-> "OE2" Residue "G ASP 378": "OD1" <-> "OD2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H ASP 20": "OD1" <-> "OD2" Residue "H TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "H ASP 118": "OD1" <-> "OD2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 174": "OD1" <-> "OD2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 249": "OD1" <-> "OD2" Residue "H ASP 271": "OD1" <-> "OD2" Residue "H GLU 306": "OE1" <-> "OE2" Residue "H PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 318": "OE1" <-> "OE2" Residue "H GLU 331": "OE1" <-> "OE2" Residue "H ASP 334": "OD1" <-> "OD2" Residue "H TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 353": "OE1" <-> "OE2" Residue "H GLU 368": "OE1" <-> "OE2" Residue "H ASP 378": "OD1" <-> "OD2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 24": "OD1" <-> "OD2" Residue "I GLU 65": "OE1" <-> "OE2" Residue "I ASP 101": "OD1" <-> "OD2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 173": "OD1" <-> "OD2" Residue "I GLU 200": "OE1" <-> "OE2" Residue "I ASP 238": "OD1" <-> "OD2" Residue "I ASP 266": "OD1" <-> "OD2" Residue "I GLU 323": "OE1" <-> "OE2" Residue "I GLU 331": "OE1" <-> "OE2" Residue "I PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 353": "OE1" <-> "OE2" Residue "I GLU 368": "OE1" <-> "OE2" Residue "I ASP 378": "OD1" <-> "OD2" Residue "L PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "L ASP 77": "OD1" <-> "OD2" Residue "L TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 116": "OD1" <-> "OD2" Residue "L ARG 147": "NH1" <-> "NH2" Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "K ARG 39": "NH1" <-> "NH2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K ARG 72": "NH1" <-> "NH2" Residue "K ASP 77": "OD1" <-> "OD2" Residue "K ASP 95": "OD1" <-> "OD2" Residue "K ASP 116": "OD1" <-> "OD2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 143": "OD1" <-> "OD2" Residue "J PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 67": "OE1" <-> "OE2" Residue "J ARG 72": "NH1" <-> "NH2" Residue "J ASP 77": "OD1" <-> "OD2" Residue "J GLU 93": "OE1" <-> "OE2" Residue "J ASP 95": "OD1" <-> "OD2" Residue "J TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 116": "OD1" <-> "OD2" Residue "J TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "J ARG 147": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28276 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2951 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain: "C" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2951 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain: "D" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "E" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "F" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2951 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 18, 'TRANS': 365} Chain: "G" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "H" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "I" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2941 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain: "L" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1194 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 6, 'TRANS': 145} Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1186 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "K" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1164 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 1 Chain: "J" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1174 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 1 Time building chain proxies: 13.96, per 1000 atoms: 0.49 Number of scatterers: 28276 At special positions: 0 Unit cell: (105.6, 124.3, 261.8, 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 136 16.00 O 5434 8.00 N 4884 7.00 C 17822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 56 " - pdb=" SG CYS L 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS K 56 " - pdb=" SG CYS K 139 " distance=2.04 Simple disulfide: pdb=" SG CYS J 56 " - pdb=" SG CYS J 139 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.80 Conformation dependent library (CDL) restraints added in 4.5 seconds 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6708 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 44 sheets defined 37.9% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'B' and resid 14 through 34 Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.768A pdb=" N ILE B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.576A pdb=" N THR B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.995A pdb=" N MET B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.753A pdb=" N ASP B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 288 removed outlier: 3.856A pdb=" N SER B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 333 Processing helix chain 'B' and resid 336 through 345 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.839A pdb=" N ALA B 356 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.630A pdb=" N ALA B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 34 Processing helix chain 'C' and resid 63 through 76 removed outlier: 3.763A pdb=" N ILE C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 removed outlier: 3.680A pdb=" N VAL C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.636A pdb=" N GLY C 155 " --> pdb=" O VAL C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.528A pdb=" N ILE C 206 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 245 through 251 removed outlier: 3.601A pdb=" N THR C 250 " --> pdb=" O ILE C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 289 removed outlier: 3.563A pdb=" N SER C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 336 through 345 Processing helix chain 'C' and resid 352 through 356 removed outlier: 4.090A pdb=" N ALA C 356 " --> pdb=" O GLU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 371 through 380 removed outlier: 4.269A pdb=" N LEU C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 34 Processing helix chain 'D' and resid 63 through 76 Processing helix chain 'D' and resid 100 through 104 removed outlier: 4.245A pdb=" N GLN D 104 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 154 removed outlier: 3.629A pdb=" N THR D 139 " --> pdb=" O PRO D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 233 through 238 removed outlier: 4.098A pdb=" N GLY D 237 " --> pdb=" O GLY D 233 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 238' Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 269 through 288 removed outlier: 3.889A pdb=" N SER D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'D' and resid 336 through 345 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.614A pdb=" N THR D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 Processing helix chain 'D' and resid 370 through 371 No H-bonds generated for 'chain 'D' and resid 370 through 371' Processing helix chain 'D' and resid 372 through 380 removed outlier: 3.700A pdb=" N ALA D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 34 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.591A pdb=" N ILE E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 135 through 155 Processing helix chain 'E' and resid 194 through 206 Processing helix chain 'E' and resid 206 through 211 Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.807A pdb=" N MET E 236 " --> pdb=" O GLY E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.750A pdb=" N THR E 250 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 288 removed outlier: 3.791A pdb=" N SER E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 333 Processing helix chain 'E' and resid 336 through 345 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.543A pdb=" N THR E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 370 through 380 removed outlier: 4.132A pdb=" N GLN E 374 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU E 375 " --> pdb=" O ASP E 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 34 Processing helix chain 'F' and resid 63 through 76 removed outlier: 3.627A pdb=" N ILE F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 83 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'F' and resid 135 through 155 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 206 through 211 Processing helix chain 'F' and resid 245 through 250 removed outlier: 4.313A pdb=" N ASP F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 245 through 250' Processing helix chain 'F' and resid 269 through 289 removed outlier: 3.610A pdb=" N SER F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 333 removed outlier: 3.518A pdb=" N PHE F 333 " --> pdb=" O VAL F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 345 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.976A pdb=" N THR F 354 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 369 Processing helix chain 'F' and resid 370 through 371 No H-bonds generated for 'chain 'F' and resid 370 through 371' Processing helix chain 'F' and resid 372 through 380 Processing helix chain 'G' and resid 14 through 34 Processing helix chain 'G' and resid 63 through 76 removed outlier: 3.590A pdb=" N ILE G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 83 Processing helix chain 'G' and resid 99 through 108 removed outlier: 4.090A pdb=" N ASN G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 154 removed outlier: 3.850A pdb=" N THR G 139 " --> pdb=" O PRO G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 Processing helix chain 'G' and resid 206 through 211 Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 245 through 251 Processing helix chain 'G' and resid 269 through 288 removed outlier: 3.939A pdb=" N SER G 273 " --> pdb=" O LYS G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 336 through 345 Processing helix chain 'G' and resid 371 through 381 removed outlier: 4.301A pdb=" N LEU G 375 " --> pdb=" O ASP G 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 381 " --> pdb=" O ARG G 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 34 Processing helix chain 'H' and resid 63 through 76 Processing helix chain 'H' and resid 80 through 83 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 135 through 154 Processing helix chain 'H' and resid 195 through 206 Processing helix chain 'H' and resid 206 through 211 Processing helix chain 'H' and resid 233 through 238 removed outlier: 3.791A pdb=" N GLY H 237 " --> pdb=" O GLY H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 250 Processing helix chain 'H' and resid 269 through 288 Processing helix chain 'H' and resid 321 through 333 Processing helix chain 'H' and resid 336 through 345 Processing helix chain 'H' and resid 350 through 356 removed outlier: 4.258A pdb=" N ALA H 356 " --> pdb=" O LYS H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 380 Processing helix chain 'I' and resid 14 through 34 Processing helix chain 'I' and resid 63 through 76 removed outlier: 3.748A pdb=" N ILE I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 106 Processing helix chain 'I' and resid 135 through 154 Processing helix chain 'I' and resid 194 through 206 Processing helix chain 'I' and resid 206 through 211 Processing helix chain 'I' and resid 245 through 250 Processing helix chain 'I' and resid 269 through 288 removed outlier: 3.743A pdb=" N SER I 273 " --> pdb=" O LYS I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 333 Processing helix chain 'I' and resid 336 through 345 Processing helix chain 'I' and resid 350 through 355 Processing helix chain 'I' and resid 365 through 369 removed outlier: 3.517A pdb=" N GLU I 368 " --> pdb=" O PHE I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 380 Processing helix chain 'L' and resid 23 through 41 removed outlier: 3.520A pdb=" N MET L 28 " --> pdb=" O ASP L 24 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA L 41 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 79 through 92 Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.959A pdb=" N ALA A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'K' and resid 24 through 41 Processing helix chain 'K' and resid 79 through 92 Processing helix chain 'J' and resid 23 through 41 Processing helix chain 'J' and resid 41 through 46 Processing helix chain 'J' and resid 79 through 92 Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 10 removed outlier: 5.393A pdb=" N ARG B 161 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N HIS B 189 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP B 163 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 187 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS B 165 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 185 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN B 167 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 183 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 169 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 179 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP B 173 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 45 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 45 removed outlier: 7.008A pdb=" N GLY B 96 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY B 54 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN B 98 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 56 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 127 removed outlier: 3.566A pdb=" N SER B 309 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 10 removed outlier: 5.849A pdb=" N ARG C 161 " --> pdb=" O HIS C 189 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N HIS C 189 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP C 163 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR C 187 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS C 165 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU C 185 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN C 167 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 183 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR C 169 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY C 179 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP C 173 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 38 through 45 Processing sheet with id=AA8, first strand: chain 'C' and resid 38 through 45 removed outlier: 7.326A pdb=" N GLY C 96 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY C 54 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLN C 98 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 56 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'C' and resid 120 through 127 removed outlier: 3.779A pdb=" N SER C 309 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 10 removed outlier: 4.143A pdb=" N GLN D 188 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP D 163 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER D 186 " --> pdb=" O ASP D 163 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS D 165 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 184 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN D 167 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA D 182 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR D 169 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE D 180 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN D 171 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 38 through 45 removed outlier: 6.745A pdb=" N VAL D 50 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA D 94 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL D 52 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY D 96 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY D 54 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 78 through 79 Processing sheet with id=AB5, first strand: chain 'D' and resid 120 through 127 Processing sheet with id=AB6, first strand: chain 'E' and resid 3 through 10 removed outlier: 3.799A pdb=" N GLN E 188 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP E 163 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER E 186 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS E 165 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL E 184 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLN E 167 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA E 182 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR E 169 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE E 180 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLN E 171 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 90 through 98 removed outlier: 6.655A pdb=" N VAL E 50 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA E 94 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL E 52 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY E 96 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY E 54 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN E 98 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE E 56 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 120 through 127 Processing sheet with id=AB9, first strand: chain 'F' and resid 2 through 10 removed outlier: 5.997A pdb=" N ARG F 161 " --> pdb=" O HIS F 189 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS F 189 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP F 163 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR F 187 " --> pdb=" O ASP F 163 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS F 165 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU F 185 " --> pdb=" O LYS F 165 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN F 167 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL F 183 " --> pdb=" O GLN F 167 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR F 169 " --> pdb=" O ASP F 181 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY F 179 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP F 173 " --> pdb=" O ILE F 177 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 90 through 94 removed outlier: 4.059A pdb=" N GLY F 54 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.734A pdb=" N HIS F 79 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 84 " --> pdb=" O HIS F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 120 through 127 Processing sheet with id=AC4, first strand: chain 'G' and resid 2 through 10 removed outlier: 7.034A pdb=" N ASP G 163 " --> pdb=" O SER G 186 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER G 186 " --> pdb=" O ASP G 163 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 165 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL G 184 " --> pdb=" O LYS G 165 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN G 167 " --> pdb=" O ALA G 182 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA G 182 " --> pdb=" O GLN G 167 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 169 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE G 180 " --> pdb=" O THR G 169 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN G 171 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LYS G 221 " --> pdb=" O GLY G 179 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP G 181 " --> pdb=" O LYS G 221 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N PHE G 223 " --> pdb=" O ASP G 181 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL G 183 " --> pdb=" O PHE G 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 90 through 93 Processing sheet with id=AC6, first strand: chain 'G' and resid 90 through 93 Processing sheet with id=AC7, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AC8, first strand: chain 'G' and resid 120 through 127 Processing sheet with id=AC9, first strand: chain 'H' and resid 5 through 10 removed outlier: 4.198A pdb=" N GLN H 188 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP H 163 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N SER H 186 " --> pdb=" O ASP H 163 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS H 165 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 184 " --> pdb=" O LYS H 165 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN H 167 " --> pdb=" O ALA H 182 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA H 182 " --> pdb=" O GLN H 167 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR H 169 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE H 180 " --> pdb=" O THR H 169 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN H 171 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 178 " --> pdb=" O GLN H 171 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 90 through 96 removed outlier: 6.285A pdb=" N VAL H 50 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA H 94 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL H 52 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY H 96 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY H 54 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 78 through 79 Processing sheet with id=AD3, first strand: chain 'H' and resid 120 through 126 Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 10 removed outlier: 5.112A pdb=" N ASP I 163 " --> pdb=" O GLN I 188 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN I 171 " --> pdb=" O ILE I 180 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE I 180 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASP I 173 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 90 through 95 Processing sheet with id=AD6, first strand: chain 'I' and resid 78 through 79 Processing sheet with id=AD7, first strand: chain 'I' and resid 120 through 127 Processing sheet with id=AD8, first strand: chain 'L' and resid 49 through 50 removed outlier: 3.965A pdb=" N LEU L 98 " --> pdb=" O VAL L 15 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 66 through 69 removed outlier: 3.501A pdb=" N ILE L 142 " --> pdb=" O PHE L 145 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.613A pdb=" N VAL A 71 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 16 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 98 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 66 through 69 removed outlier: 3.905A pdb=" N ILE A 142 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 47 through 50 Processing sheet with id=AE4, first strand: chain 'K' and resid 47 through 50 Processing sheet with id=AE5, first strand: chain 'K' and resid 126 through 129 removed outlier: 5.151A pdb=" N ARG K 148 " --> pdb=" O GLN K 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 47 through 48 removed outlier: 3.896A pdb=" N LEU J 98 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 66 through 69 Processing sheet with id=AE8, first strand: chain 'J' and resid 126 through 129 removed outlier: 4.901A pdb=" N PHE J 127 " --> pdb=" O GLN J 150 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN J 150 " --> pdb=" O PHE J 127 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3645 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: 9.33 Time building geometry restraints manager: 10.83 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: 9517 1.34 - 1.46: 5422 1.46 - 1.57: 13694 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 28849 Sorted by residual: bond pdb=" C ILE G 210 " pdb=" N LEU G 211 " ideal model delta sigma weight residual 1.331 1.285 0.046 2.07e-02 2.33e+03 4.86e+00 bond pdb=" CB PHE B 84 " pdb=" CG PHE B 84 " ideal model delta sigma weight residual 1.502 1.453 0.049 2.30e-02 1.89e+03 4.46e+00 bond pdb=" CA HIS C 189 " pdb=" CB HIS C 189 " ideal model delta sigma weight residual 1.535 1.493 0.043 2.09e-02 2.29e+03 4.15e+00 bond pdb=" CA PHE D 360 " pdb=" CB PHE D 360 " ideal model delta sigma weight residual 1.534 1.504 0.030 1.57e-02 4.06e+03 3.65e+00 bond pdb=" CB PHE A 3 " pdb=" CG PHE A 3 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.60e+00 ... (remaining 28844 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.59: 618 105.59 - 112.76: 15834 112.76 - 119.92: 9428 119.92 - 127.08: 12887 127.08 - 134.24: 332 Bond angle restraints: 39099 Sorted by residual: angle pdb=" N VAL H 132 " pdb=" CA VAL H 132 " pdb=" C VAL H 132 " ideal model delta sigma weight residual 112.83 106.65 6.18 9.90e-01 1.02e+00 3.90e+01 angle pdb=" CA CYS L 139 " pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " ideal model delta sigma weight residual 114.40 127.45 -13.05 2.30e+00 1.89e-01 3.22e+01 angle pdb=" N VAL I 132 " pdb=" CA VAL I 132 " pdb=" C VAL I 132 " ideal model delta sigma weight residual 111.91 107.25 4.66 8.90e-01 1.26e+00 2.75e+01 angle pdb=" CA CYS K 56 " pdb=" CB CYS K 56 " pdb=" SG CYS K 56 " ideal model delta sigma weight residual 114.40 124.54 -10.14 2.30e+00 1.89e-01 1.94e+01 angle pdb=" CA CYS L 56 " pdb=" CB CYS L 56 " pdb=" SG CYS L 56 " ideal model delta sigma weight residual 114.40 124.36 -9.96 2.30e+00 1.89e-01 1.88e+01 ... (remaining 39094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 15535 18.06 - 36.12: 1467 36.12 - 54.18: 236 54.18 - 72.24: 48 72.24 - 90.30: 42 Dihedral angle restraints: 17328 sinusoidal: 6848 harmonic: 10480 Sorted by residual: dihedral pdb=" CB CYS A 56 " pdb=" SG CYS A 56 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual -86.00 -0.06 -85.94 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS J 56 " pdb=" SG CYS J 56 " pdb=" SG CYS J 139 " pdb=" CB CYS J 139 " ideal model delta sinusoidal sigma weight residual -86.00 -6.41 -79.59 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CA CYS L 23 " pdb=" C CYS L 23 " pdb=" N ASP L 24 " pdb=" CA ASP L 24 " ideal model delta harmonic sigma weight residual -180.00 -147.83 -32.17 0 5.00e+00 4.00e-02 4.14e+01 ... (remaining 17325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3056 0.042 - 0.085: 975 0.085 - 0.127: 290 0.127 - 0.169: 30 0.169 - 0.211: 8 Chirality restraints: 4359 Sorted by residual: chirality pdb=" CB ILE L 61 " pdb=" CA ILE L 61 " pdb=" CG1 ILE L 61 " pdb=" CG2 ILE L 61 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLU K 6 " pdb=" N GLU K 6 " pdb=" C GLU K 6 " pdb=" CB GLU K 6 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" C PRO C 162 " pdb=" CB PRO C 162 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 4356 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 123 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO L 124 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 124 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 124 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 130 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO J 131 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO J 131 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO J 131 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET G 134 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO G 135 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 135 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 135 " -0.031 5.00e-02 4.00e+02 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 675 2.57 - 3.15: 28772 3.15 - 3.74: 50507 3.74 - 4.32: 69128 4.32 - 4.90: 105435 Nonbonded interactions: 254517 Sorted by model distance: nonbonded pdb=" O TYR I 125 " pdb=" OH TYR I 251 " model vdw 1.988 2.440 nonbonded pdb=" OD1 ASP B 194 " pdb=" OG SER B 197 " model vdw 1.998 2.440 nonbonded pdb=" O GLN A 128 " pdb=" NH1 ARG A 147 " model vdw 2.018 2.520 nonbonded pdb=" OD1 ASP F 194 " pdb=" OG SER F 197 " model vdw 2.026 2.440 nonbonded pdb=" OG SER B 299 " pdb=" OG1 THR B 308 " model vdw 2.044 2.440 ... (remaining 254512 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' and (resid 3 through 59 or resid 65 through 153)) selection = (chain 'J' and (resid 3 through 59 or resid 65 through 153)) selection = (chain 'K' and resid 3 through 153) selection = (chain 'L' and (resid 3 through 59 or resid 65 through 153)) } ncs_group { reference = (chain 'B' and resid 1 through 383) selection = (chain 'C' and resid 1 through 383) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 1 through 383) 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: 1.250 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: 7.120 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 70.020 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4191 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 : 0.008 0.058 28849 Z= 0.506 Angle : 0.863 13.048 39099 Z= 0.503 Chirality : 0.045 0.211 4359 Planarity : 0.005 0.064 5118 Dihedral : 14.977 90.301 10608 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 36.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 0.20 % Allowed : 9.45 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.12), residues: 3638 helix: -2.36 (0.12), residues: 1148 sheet: -0.78 (0.17), residues: 798 loop : -2.16 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 159 HIS 0.011 0.003 HIS G 364 PHE 0.032 0.002 PHE K 140 TYR 0.027 0.003 TYR K 100 ARG 0.012 0.001 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 498 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 PRO cc_start: 0.3760 (Cg_exo) cc_final: 0.3160 (Cg_endo) REVERT: B 343 MET cc_start: 0.3541 (ttp) cc_final: 0.3271 (mtp) REVERT: E 185 LEU cc_start: 0.7472 (tp) cc_final: 0.6960 (mp) REVERT: G 185 LEU cc_start: 0.7767 (tt) cc_final: 0.7528 (mt) REVERT: I 215 TRP cc_start: 0.7380 (m-10) cc_final: 0.7026 (m-10) REVERT: I 345 ASP cc_start: 0.7996 (t0) cc_final: 0.7757 (t0) REVERT: L 28 MET cc_start: 0.9058 (mmm) cc_final: 0.8202 (tpp) REVERT: L 53 LEU cc_start: 0.5538 (tp) cc_final: 0.4845 (tp) REVERT: L 56 CYS cc_start: 0.0349 (OUTLIER) cc_final: -0.0157 (m) REVERT: L 83 ASN cc_start: 0.9242 (t0) cc_final: 0.9036 (t0) REVERT: L 87 LEU cc_start: 0.8466 (mt) cc_final: 0.8006 (mt) REVERT: L 142 ILE cc_start: 0.5470 (tt) cc_final: 0.4603 (tt) REVERT: K 12 TYR cc_start: 0.1790 (m-80) cc_final: 0.0579 (m-80) REVERT: K 13 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.6509 (m) REVERT: K 98 LEU cc_start: 0.6676 (mp) cc_final: 0.5755 (tt) REVERT: K 127 PHE cc_start: 0.5151 (t80) cc_final: 0.4344 (t80) REVERT: J 109 LEU cc_start: 0.6376 (pt) cc_final: 0.5529 (pt) outliers start: 6 outliers final: 2 residues processed: 504 average time/residue: 0.4576 time to fit residues: 343.5289 Evaluate side-chains 280 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 276 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 56 CYS Chi-restraints excluded: chain J residue 139 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 146 optimal weight: 0.3980 chunk 283 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 328 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 GLN B 195 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS C 21 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 195 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 HIS ** E 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN E 195 GLN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN F 104 GLN ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 297 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS G 14 HIS G 70 ASN G 79 HIS G 146 GLN G 171 GLN ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS H 87 ASN H 98 GLN H 103 ASN H 104 GLN H 114 GLN ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 225 ASN H 257 HIS H 348 HIS I 33 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 ASN ** I 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 ASN L 94 GLN ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 HIS ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN K 150 GLN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4786 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28849 Z= 0.295 Angle : 0.787 12.138 39099 Z= 0.412 Chirality : 0.047 0.197 4359 Planarity : 0.006 0.134 5118 Dihedral : 5.952 55.288 3964 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.70 % Favored : 95.16 % Rotamer: Outliers : 3.00 % Allowed : 16.29 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.30 (0.13), residues: 3638 helix: -0.45 (0.14), residues: 1155 sheet: -0.12 (0.18), residues: 766 loop : -1.46 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 149 HIS 0.013 0.002 HIS D 14 PHE 0.023 0.003 PHE I 230 TYR 0.029 0.003 TYR E 280 ARG 0.013 0.001 ARG K 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 318 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 310 ILE cc_start: 0.1881 (OUTLIER) cc_final: 0.1064 (pt) REVERT: B 343 MET cc_start: 0.3263 (ttp) cc_final: 0.2890 (mtp) REVERT: C 5 PHE cc_start: 0.5724 (t80) cc_final: 0.5508 (t80) REVERT: C 323 GLU cc_start: 0.7731 (mp0) cc_final: 0.7517 (pm20) REVERT: D 246 ILE cc_start: 0.6474 (OUTLIER) cc_final: 0.6156 (mp) REVERT: D 365 PHE cc_start: 0.1040 (m-80) cc_final: 0.0715 (m-80) REVERT: E 353 GLU cc_start: 0.5382 (OUTLIER) cc_final: 0.4816 (pt0) REVERT: G 30 ILE cc_start: 0.3409 (OUTLIER) cc_final: 0.3045 (tp) REVERT: G 46 LYS cc_start: 0.7284 (tppt) cc_final: 0.6681 (tttp) REVERT: G 185 LEU cc_start: 0.8060 (tt) cc_final: 0.7716 (mt) REVERT: H 173 ASP cc_start: 0.8823 (m-30) cc_final: 0.8395 (p0) REVERT: I 49 MET cc_start: 0.3330 (tmm) cc_final: 0.2862 (tpt) REVERT: I 82 MET cc_start: 0.2139 (mmt) cc_final: 0.1687 (mmm) REVERT: I 215 TRP cc_start: 0.7599 (m-10) cc_final: 0.7203 (m-10) REVERT: I 345 ASP cc_start: 0.8026 (t0) cc_final: 0.7531 (t0) REVERT: L 28 MET cc_start: 0.8969 (mmm) cc_final: 0.8157 (tpp) REVERT: L 34 MET cc_start: 0.6801 (mtt) cc_final: 0.6485 (mtt) REVERT: L 141 THR cc_start: -0.2504 (OUTLIER) cc_final: -0.2848 (m) REVERT: L 143 ASP cc_start: 0.8693 (t70) cc_final: 0.8357 (t70) REVERT: A 28 MET cc_start: 0.8567 (tpp) cc_final: 0.8314 (tpp) REVERT: K 127 PHE cc_start: 0.5195 (t80) cc_final: 0.4578 (t80) outliers start: 90 outliers final: 55 residues processed: 390 average time/residue: 0.4452 time to fit residues: 270.7109 Evaluate side-chains 305 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 245 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 147 ARG Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 49 MET Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 293 ARG Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 139 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 30.0000 chunk 102 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 329 optimal weight: 9.9990 chunk 355 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 326 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 264 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 167 GLN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN F 171 GLN ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS G 142 HIS ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 GLN I 3 HIS ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 HIS L 31 HIS ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5480 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 28849 Z= 0.421 Angle : 0.955 18.957 39099 Z= 0.499 Chirality : 0.052 0.355 4359 Planarity : 0.008 0.111 5118 Dihedral : 6.540 53.792 3962 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 46.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.71 % Rotamer: Outliers : 6.24 % Allowed : 17.76 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3638 helix: -0.67 (0.14), residues: 1165 sheet: -0.52 (0.18), residues: 788 loop : -1.55 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP F 367 HIS 0.062 0.003 HIS F 359 PHE 0.032 0.004 PHE A 140 TYR 0.036 0.004 TYR E 351 ARG 0.031 0.002 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 294 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.2933 (tpp) cc_final: 0.2241 (mpp) REVERT: B 310 ILE cc_start: 0.4818 (OUTLIER) cc_final: 0.3809 (pt) REVERT: B 343 MET cc_start: 0.3668 (ttp) cc_final: 0.2759 (mtp) REVERT: C 123 PHE cc_start: 0.4221 (m-80) cc_final: -0.0531 (m-80) REVERT: D 246 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7225 (mp) REVERT: D 329 VAL cc_start: 0.8574 (t) cc_final: 0.8369 (p) REVERT: E 51 LEU cc_start: 0.8119 (tt) cc_final: 0.7823 (mm) REVERT: E 92 LEU cc_start: 0.3919 (OUTLIER) cc_final: 0.3691 (mm) REVERT: E 353 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5581 (pt0) REVERT: F 224 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7159 (pt) REVERT: F 330 ARG cc_start: 0.6591 (mtm110) cc_final: 0.6178 (mmt90) REVERT: F 360 PHE cc_start: 0.6889 (m-80) cc_final: 0.6674 (m-80) REVERT: F 367 TRP cc_start: 0.7805 (p90) cc_final: 0.6962 (p90) REVERT: G 30 ILE cc_start: 0.4084 (OUTLIER) cc_final: 0.3879 (tp) REVERT: G 46 LYS cc_start: 0.7634 (tppt) cc_final: 0.6649 (tttt) REVERT: G 185 LEU cc_start: 0.8213 (tt) cc_final: 0.7994 (mt) REVERT: G 311 MET cc_start: 0.4799 (tmm) cc_final: 0.2626 (tpt) REVERT: G 343 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.5383 (ptt) REVERT: H 14 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.8073 (m-70) REVERT: H 173 ASP cc_start: 0.8815 (m-30) cc_final: 0.8308 (p0) REVERT: H 176 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8534 (tptp) REVERT: I 84 PHE cc_start: 0.7012 (t80) cc_final: 0.6464 (t80) REVERT: I 134 MET cc_start: 0.3208 (mmm) cc_final: 0.2443 (mmm) REVERT: I 215 TRP cc_start: 0.7978 (m-10) cc_final: 0.7663 (m-10) REVERT: I 254 MET cc_start: 0.5590 (tpt) cc_final: 0.4452 (tmm) REVERT: I 262 PHE cc_start: 0.5625 (m-80) cc_final: 0.5283 (m-10) REVERT: I 345 ASP cc_start: 0.7888 (t0) cc_final: 0.7619 (t0) REVERT: L 28 MET cc_start: 0.8935 (mmm) cc_final: 0.8199 (tpp) REVERT: L 139 CYS cc_start: 0.1377 (OUTLIER) cc_final: 0.0190 (m) REVERT: L 140 PHE cc_start: 0.7159 (m-10) cc_final: 0.6829 (m-10) REVERT: L 145 PHE cc_start: 0.7495 (m-80) cc_final: 0.7086 (m-80) REVERT: L 147 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8094 (ptt90) REVERT: K 13 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.7011 (t) REVERT: J 34 MET cc_start: 0.6606 (mtt) cc_final: 0.4173 (mtt) REVERT: J 109 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6354 (pp) outliers start: 187 outliers final: 91 residues processed: 448 average time/residue: 0.4031 time to fit residues: 284.1452 Evaluate side-chains 343 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 239 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 378 ASP Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain G residue 293 ARG Chi-restraints excluded: chain G residue 343 MET Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 176 LYS Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 139 CYS Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 18 PHE Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 72 ARG Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 139 CYS Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 150 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 0.0980 chunk 247 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 330 optimal weight: 20.0000 chunk 349 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 313 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS B 21 GLN B 87 ASN B 297 GLN B 359 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS F 167 GLN F 171 GLN ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28849 Z= 0.251 Angle : 0.751 14.349 39099 Z= 0.384 Chirality : 0.046 0.191 4359 Planarity : 0.006 0.066 5118 Dihedral : 5.882 40.510 3961 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 33.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.80 % Rotamer: Outliers : 4.71 % Allowed : 20.46 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.16 (0.14), residues: 3638 helix: -0.10 (0.15), residues: 1164 sheet: -0.41 (0.18), residues: 795 loop : -1.38 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 215 HIS 0.013 0.002 HIS F 359 PHE 0.021 0.002 PHE F 315 TYR 0.034 0.002 TYR C 44 ARG 0.011 0.001 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 264 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.8009 (mmm) cc_final: 0.7796 (mmm) REVERT: B 343 MET cc_start: 0.3510 (ttp) cc_final: 0.2641 (mtp) REVERT: C 157 LEU cc_start: 0.7505 (tp) cc_final: 0.7203 (tt) REVERT: E 353 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6506 (pt0) REVERT: F 330 ARG cc_start: 0.6733 (mtm110) cc_final: 0.6361 (mmt90) REVERT: G 46 LYS cc_start: 0.7570 (tppt) cc_final: 0.6703 (tttt) REVERT: G 236 MET cc_start: 0.3618 (mmm) cc_final: 0.3397 (mmm) REVERT: H 89 CYS cc_start: 0.6990 (t) cc_final: 0.6636 (m) REVERT: H 173 ASP cc_start: 0.8871 (m-30) cc_final: 0.8409 (p0) REVERT: I 56 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8328 (mm) REVERT: I 84 PHE cc_start: 0.6749 (t80) cc_final: 0.6466 (t80) REVERT: I 134 MET cc_start: 0.3447 (mmm) cc_final: 0.2914 (mmm) REVERT: I 262 PHE cc_start: 0.5624 (m-80) cc_final: 0.5361 (m-80) REVERT: I 345 ASP cc_start: 0.7908 (t0) cc_final: 0.7626 (t0) REVERT: L 28 MET cc_start: 0.8988 (mmm) cc_final: 0.8431 (tpp) REVERT: L 145 PHE cc_start: 0.7551 (m-80) cc_final: 0.7294 (m-80) REVERT: L 147 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7918 (ptt90) REVERT: A 12 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.5270 (t80) REVERT: K 13 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.6086 (t) REVERT: K 29 SER cc_start: 0.8913 (t) cc_final: 0.7766 (p) REVERT: K 33 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7088 (m-70) REVERT: J 109 LEU cc_start: 0.6827 (pt) cc_final: 0.6452 (pp) REVERT: J 149 TRP cc_start: 0.3790 (OUTLIER) cc_final: 0.2673 (p-90) outliers start: 141 outliers final: 82 residues processed: 380 average time/residue: 0.3915 time to fit residues: 237.4913 Evaluate side-chains 320 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 231 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 343 MET Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 PHE Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 0.0050 chunk 198 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 chunk 241 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 314 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28849 Z= 0.233 Angle : 0.733 13.738 39099 Z= 0.371 Chirality : 0.046 0.189 4359 Planarity : 0.005 0.057 5118 Dihedral : 5.707 52.310 3961 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 32.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.66 % Favored : 94.23 % Rotamer: Outliers : 4.31 % Allowed : 21.26 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3638 helix: 0.12 (0.15), residues: 1179 sheet: -0.40 (0.18), residues: 795 loop : -1.27 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 367 HIS 0.012 0.001 HIS L 31 PHE 0.035 0.002 PHE F 360 TYR 0.031 0.002 TYR C 44 ARG 0.012 0.001 ARG E 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 253 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5078 (t80) REVERT: B 203 MET cc_start: 0.7887 (mmm) cc_final: 0.7674 (mmm) REVERT: B 343 MET cc_start: 0.3985 (ttp) cc_final: 0.3028 (mtp) REVERT: C 49 MET cc_start: 0.5083 (mmm) cc_final: 0.4755 (mmm) REVERT: C 144 LEU cc_start: 0.7847 (mt) cc_final: 0.7508 (mt) REVERT: C 157 LEU cc_start: 0.7587 (tp) cc_final: 0.6877 (tt) REVERT: F 134 MET cc_start: 0.4315 (mmt) cc_final: 0.4115 (mmm) REVERT: G 311 MET cc_start: 0.4588 (tmm) cc_final: 0.2502 (tpt) REVERT: G 343 MET cc_start: 0.5450 (ptt) cc_final: 0.4917 (ptp) REVERT: H 89 CYS cc_start: 0.6992 (t) cc_final: 0.6522 (m) REVERT: H 173 ASP cc_start: 0.8893 (m-30) cc_final: 0.8406 (p0) REVERT: I 82 MET cc_start: 0.1748 (mmt) cc_final: 0.1529 (mmp) REVERT: I 84 PHE cc_start: 0.6827 (t80) cc_final: 0.6517 (t80) REVERT: I 345 ASP cc_start: 0.7900 (t0) cc_final: 0.7614 (t0) REVERT: L 28 MET cc_start: 0.8918 (mmm) cc_final: 0.8358 (tpp) REVERT: A 12 TYR cc_start: 0.5593 (OUTLIER) cc_final: 0.5263 (t80) REVERT: K 33 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.6952 (m170) REVERT: K 78 LYS cc_start: 0.7881 (tmtt) cc_final: 0.7372 (mmmt) REVERT: K 80 GLN cc_start: 0.6962 (tm-30) cc_final: 0.6538 (tm-30) REVERT: J 109 LEU cc_start: 0.6973 (pt) cc_final: 0.6507 (pp) REVERT: J 149 TRP cc_start: 0.3911 (OUTLIER) cc_final: 0.2732 (p-90) outliers start: 129 outliers final: 84 residues processed: 358 average time/residue: 0.3842 time to fit residues: 221.2062 Evaluate side-chains 310 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 222 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 86 optimal weight: 0.0000 chunk 350 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN F 297 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28849 Z= 0.208 Angle : 0.717 12.576 39099 Z= 0.361 Chirality : 0.045 0.203 4359 Planarity : 0.005 0.056 5118 Dihedral : 5.533 50.605 3961 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 30.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 4.24 % Allowed : 21.83 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3638 helix: 0.39 (0.15), residues: 1175 sheet: -0.35 (0.18), residues: 772 loop : -1.23 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP L 92 HIS 0.007 0.001 HIS G 359 PHE 0.025 0.002 PHE F 315 TYR 0.038 0.002 TYR K 12 ARG 0.011 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 248 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5145 (t80) REVERT: B 82 MET cc_start: -0.0140 (mmt) cc_final: -0.0706 (mmm) REVERT: B 343 MET cc_start: 0.4087 (ttp) cc_final: 0.2944 (mtp) REVERT: C 144 LEU cc_start: 0.7819 (mt) cc_final: 0.7473 (mt) REVERT: C 236 MET cc_start: 0.3260 (mmm) cc_final: 0.2995 (mmm) REVERT: G 44 TYR cc_start: 0.6055 (m-80) cc_final: 0.5446 (m-80) REVERT: G 236 MET cc_start: 0.3125 (mmm) cc_final: 0.2881 (mmm) REVERT: G 311 MET cc_start: 0.4709 (tmm) cc_final: 0.2969 (tpt) REVERT: G 343 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.5301 (ptt) REVERT: H 89 CYS cc_start: 0.7081 (t) cc_final: 0.6592 (m) REVERT: H 173 ASP cc_start: 0.8891 (m-30) cc_final: 0.8401 (p0) REVERT: I 345 ASP cc_start: 0.7872 (t0) cc_final: 0.7575 (t0) REVERT: L 28 MET cc_start: 0.8970 (mmm) cc_final: 0.8352 (tpp) REVERT: L 143 ASP cc_start: 0.9162 (t70) cc_final: 0.8956 (t0) REVERT: L 145 PHE cc_start: 0.7293 (m-80) cc_final: 0.6876 (m-80) REVERT: A 12 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.5303 (t80) REVERT: K 33 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.6952 (m170) REVERT: K 78 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7522 (mmmt) REVERT: K 80 GLN cc_start: 0.6766 (tm-30) cc_final: 0.6316 (tm-30) REVERT: J 12 TYR cc_start: 0.5284 (m-80) cc_final: 0.4728 (m-80) REVERT: J 109 LEU cc_start: 0.6953 (pt) cc_final: 0.6517 (pp) REVERT: J 149 TRP cc_start: 0.3861 (OUTLIER) cc_final: 0.2596 (p-90) outliers start: 127 outliers final: 90 residues processed: 351 average time/residue: 0.3847 time to fit residues: 219.0714 Evaluate side-chains 320 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 225 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 343 MET Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 14 HIS Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 294 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 348 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.8201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 28849 Z= 0.292 Angle : 0.788 14.171 39099 Z= 0.403 Chirality : 0.047 0.239 4359 Planarity : 0.006 0.054 5118 Dihedral : 5.797 49.087 3961 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 37.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.62 % Rotamer: Outliers : 4.87 % Allowed : 22.03 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3638 helix: 0.13 (0.15), residues: 1187 sheet: -0.61 (0.18), residues: 791 loop : -1.34 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP E 367 HIS 0.015 0.002 HIS L 31 PHE 0.034 0.003 PHE D 365 TYR 0.027 0.002 TYR C 44 ARG 0.009 0.001 ARG L 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 234 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.0489 (mmt) cc_final: -0.0196 (mmm) REVERT: B 343 MET cc_start: 0.4246 (ttp) cc_final: 0.3230 (mtp) REVERT: C 144 LEU cc_start: 0.7960 (mt) cc_final: 0.7614 (mt) REVERT: D 46 LYS cc_start: 0.7754 (tppt) cc_final: 0.7401 (tttt) REVERT: D 122 MET cc_start: 0.5638 (mtt) cc_final: 0.5347 (mtt) REVERT: E 353 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7075 (pt0) REVERT: F 330 ARG cc_start: 0.7604 (mtm110) cc_final: 0.7100 (mmt90) REVERT: G 44 TYR cc_start: 0.6270 (m-80) cc_final: 0.5336 (m-80) REVERT: G 236 MET cc_start: 0.3530 (mmm) cc_final: 0.3252 (mmm) REVERT: G 311 MET cc_start: 0.4994 (tmm) cc_final: 0.3328 (tpt) REVERT: G 343 MET cc_start: 0.5754 (OUTLIER) cc_final: 0.5160 (ptp) REVERT: H 173 ASP cc_start: 0.8971 (m-30) cc_final: 0.8526 (p0) REVERT: I 215 TRP cc_start: 0.8064 (m-10) cc_final: 0.7780 (m-10) REVERT: I 345 ASP cc_start: 0.7865 (t0) cc_final: 0.7586 (t0) REVERT: L 28 MET cc_start: 0.8923 (mmm) cc_final: 0.8276 (tpp) REVERT: L 143 ASP cc_start: 0.8923 (t70) cc_final: 0.8648 (t0) REVERT: L 145 PHE cc_start: 0.7068 (m-80) cc_final: 0.6086 (m-80) REVERT: L 147 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8013 (ptt90) REVERT: A 12 TYR cc_start: 0.5741 (OUTLIER) cc_final: 0.5439 (t80) REVERT: K 28 MET cc_start: 0.8998 (mmm) cc_final: 0.8776 (mmm) REVERT: K 33 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.7042 (m170) REVERT: K 80 GLN cc_start: 0.6787 (tm-30) cc_final: 0.6333 (tm-30) REVERT: J 12 TYR cc_start: 0.5606 (m-80) cc_final: 0.5198 (m-80) REVERT: J 109 LEU cc_start: 0.7111 (pt) cc_final: 0.6706 (pp) REVERT: J 149 TRP cc_start: 0.4053 (OUTLIER) cc_final: 0.2622 (p-90) outliers start: 146 outliers final: 106 residues processed: 357 average time/residue: 0.4144 time to fit residues: 239.9705 Evaluate side-chains 324 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 212 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain G residue 343 MET Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 375 LEU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 141 THR Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 92 TRP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 33 HIS Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 208 optimal weight: 0.0050 chunk 105 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 237 optimal weight: 0.0370 chunk 172 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 overall best weight: 2.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 GLN ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 257 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.8483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 28849 Z= 0.217 Angle : 0.738 14.033 39099 Z= 0.370 Chirality : 0.045 0.217 4359 Planarity : 0.005 0.065 5118 Dihedral : 5.624 50.393 3961 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 31.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.47 % Rotamer: Outliers : 3.84 % Allowed : 23.40 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3638 helix: 0.41 (0.15), residues: 1183 sheet: -0.47 (0.18), residues: 770 loop : -1.28 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 367 HIS 0.024 0.002 HIS K 33 PHE 0.043 0.002 PHE L 11 TYR 0.026 0.002 TYR C 44 ARG 0.010 0.001 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 226 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.0360 (mmt) cc_final: 0.0006 (mmm) REVERT: B 343 MET cc_start: 0.4102 (ttp) cc_final: 0.3185 (mtp) REVERT: C 144 LEU cc_start: 0.7983 (mt) cc_final: 0.7631 (mt) REVERT: C 236 MET cc_start: 0.1974 (mmm) cc_final: 0.1766 (mmm) REVERT: C 343 MET cc_start: 0.6264 (ttm) cc_final: 0.5043 (ptm) REVERT: D 46 LYS cc_start: 0.7658 (tppt) cc_final: 0.7278 (tttt) REVERT: D 122 MET cc_start: 0.5379 (mtt) cc_final: 0.5104 (mtt) REVERT: D 343 MET cc_start: 0.6936 (tmm) cc_final: 0.6651 (ppp) REVERT: E 101 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6229 (m-30) REVERT: E 236 MET cc_start: 0.5229 (mmt) cc_final: 0.4574 (mmt) REVERT: F 330 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7150 (mmt90) REVERT: G 44 TYR cc_start: 0.6362 (m-80) cc_final: 0.5359 (m-80) REVERT: G 72 VAL cc_start: 0.9104 (t) cc_final: 0.8890 (m) REVERT: G 343 MET cc_start: 0.5874 (OUTLIER) cc_final: 0.5306 (ptt) REVERT: H 173 ASP cc_start: 0.9010 (m-30) cc_final: 0.8554 (p0) REVERT: I 215 TRP cc_start: 0.8090 (m-10) cc_final: 0.7778 (m-10) REVERT: I 345 ASP cc_start: 0.7838 (t0) cc_final: 0.7552 (t0) REVERT: L 28 MET cc_start: 0.8919 (mmm) cc_final: 0.8244 (tpp) REVERT: L 143 ASP cc_start: 0.9032 (t70) cc_final: 0.8738 (t0) REVERT: L 145 PHE cc_start: 0.7130 (m-80) cc_final: 0.6421 (m-80) REVERT: A 12 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.5281 (t80) REVERT: K 78 LYS cc_start: 0.8142 (tmtt) cc_final: 0.7864 (mmmt) REVERT: K 80 GLN cc_start: 0.6930 (tm-30) cc_final: 0.6462 (tm-30) REVERT: J 149 TRP cc_start: 0.3941 (OUTLIER) cc_final: 0.2386 (p-90) outliers start: 115 outliers final: 94 residues processed: 322 average time/residue: 0.3890 time to fit residues: 201.4303 Evaluate side-chains 310 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 212 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 257 HIS Chi-restraints excluded: chain G residue 343 MET Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 8.9990 chunk 334 optimal weight: 7.9990 chunk 304 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 293 optimal weight: 40.0000 chunk 307 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 ASN G 257 HIS ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS ** I 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 1.0472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 28849 Z= 0.395 Angle : 0.970 20.192 39099 Z= 0.505 Chirality : 0.054 0.448 4359 Planarity : 0.008 0.126 5118 Dihedral : 6.710 51.135 3961 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 54.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.75 % Favored : 92.17 % Rotamer: Outliers : 4.34 % Allowed : 23.77 % Favored : 71.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 3638 helix: -0.51 (0.14), residues: 1188 sheet: -1.11 (0.18), residues: 774 loop : -1.70 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP E 367 HIS 0.077 0.004 HIS G 257 PHE 0.044 0.004 PHE D 365 TYR 0.037 0.004 TYR A 118 ARG 0.074 0.002 ARG G 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 223 time to evaluate : 3.239 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: B 343 MET cc_start: 0.4553 (ttp) cc_final: 0.4003 (ttm) REVERT: C 44 TYR cc_start: 0.5322 (t80) cc_final: 0.4938 (t80) REVERT: C 49 MET cc_start: 0.6743 (mmm) cc_final: 0.6336 (mmm) REVERT: C 51 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7506 (pp) REVERT: C 140 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7238 (t80) REVERT: C 144 LEU cc_start: 0.8227 (mt) cc_final: 0.7837 (mt) REVERT: C 343 MET cc_start: 0.7447 (ttm) cc_final: 0.6799 (ptm) REVERT: D 46 LYS cc_start: 0.8271 (tppt) cc_final: 0.7513 (tttt) REVERT: D 122 MET cc_start: 0.6166 (mtt) cc_final: 0.5664 (mtt) REVERT: E 101 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: E 236 MET cc_start: 0.5600 (mmt) cc_final: 0.5004 (mmt) REVERT: E 367 TRP cc_start: 0.7608 (p90) cc_final: 0.7154 (p90) REVERT: F 51 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8163 (mm) REVERT: F 122 MET cc_start: 0.4509 (mtt) cc_final: 0.4220 (mtm) REVERT: F 236 MET cc_start: 0.7140 (mmt) cc_final: 0.6857 (mmt) REVERT: F 330 ARG cc_start: 0.8357 (mtm110) cc_final: 0.7635 (mmt90) REVERT: G 46 LYS cc_start: 0.7870 (tppt) cc_final: 0.6952 (tmtt) REVERT: G 236 MET cc_start: 0.4323 (mmm) cc_final: 0.3788 (mmm) REVERT: G 311 MET cc_start: 0.5713 (tmm) cc_final: 0.4282 (tpt) REVERT: H 113 GLU cc_start: 0.7805 (tp30) cc_final: 0.7506 (mp0) REVERT: I 345 ASP cc_start: 0.7961 (t0) cc_final: 0.7640 (t0) REVERT: L 28 MET cc_start: 0.8814 (mmm) cc_final: 0.8284 (tpp) REVERT: L 34 MET cc_start: 0.6300 (mtt) cc_final: 0.5907 (mtt) REVERT: L 143 ASP cc_start: 0.8793 (t70) cc_final: 0.8491 (t0) REVERT: L 147 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8144 (ptt180) REVERT: A 12 TYR cc_start: 0.5825 (OUTLIER) cc_final: 0.5590 (t80) REVERT: A 15 VAL cc_start: 0.7770 (m) cc_final: 0.7447 (p) REVERT: K 80 GLN cc_start: 0.7029 (tm-30) cc_final: 0.6585 (tm-30) REVERT: J 149 TRP cc_start: 0.4981 (OUTLIER) cc_final: 0.3246 (p-90) outliers start: 130 outliers final: 99 residues processed: 329 average time/residue: 0.4034 time to fit residues: 215.6910 Evaluate side-chains 308 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 202 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 343 MET Chi-restraints excluded: chain G residue 367 TRP Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 375 LEU Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain L residue 31 HIS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 12 TYR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 75 CYS Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 7.9990 chunk 343 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 239 optimal weight: 0.9990 chunk 360 optimal weight: 10.0000 chunk 331 optimal weight: 5.9990 chunk 287 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 176 optimal weight: 0.1980 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 GLN ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 1.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28849 Z= 0.272 Angle : 0.826 14.739 39099 Z= 0.414 Chirality : 0.048 0.251 4359 Planarity : 0.006 0.140 5118 Dihedral : 6.201 51.594 3961 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 37.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 3.30 % Allowed : 25.57 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3638 helix: -0.07 (0.15), residues: 1179 sheet: -0.98 (0.18), residues: 757 loop : -1.56 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP I 215 HIS 0.014 0.002 HIS F 364 PHE 0.034 0.002 PHE D 365 TYR 0.035 0.002 TYR L 12 ARG 0.008 0.001 ARG D 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7276 Ramachandran restraints generated. 3638 Oldfield, 0 Emsley, 3638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 217 time to evaluate : 3.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.0708 (mmt) cc_final: 0.0404 (mmm) REVERT: B 187 THR cc_start: 0.7678 (t) cc_final: 0.7263 (t) REVERT: B 343 MET cc_start: 0.4718 (ttp) cc_final: 0.4188 (ptp) REVERT: C 44 TYR cc_start: 0.4841 (t80) cc_final: 0.4609 (t80) REVERT: C 140 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7398 (t80) REVERT: C 144 LEU cc_start: 0.8276 (mt) cc_final: 0.7903 (mt) REVERT: C 343 MET cc_start: 0.7510 (ttm) cc_final: 0.6722 (ptm) REVERT: D 46 LYS cc_start: 0.8169 (tppt) cc_final: 0.7012 (tttt) REVERT: D 122 MET cc_start: 0.6258 (mtt) cc_final: 0.5834 (mtt) REVERT: D 311 MET cc_start: 0.5741 (tmm) cc_final: 0.4696 (tpp) REVERT: E 101 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: F 51 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8129 (mm) REVERT: F 122 MET cc_start: 0.4433 (mtt) cc_final: 0.4119 (mtm) REVERT: F 236 MET cc_start: 0.7191 (mmt) cc_final: 0.6936 (mmt) REVERT: F 295 GLU cc_start: 0.7352 (tt0) cc_final: 0.6341 (tp30) REVERT: F 330 ARG cc_start: 0.8444 (mtm110) cc_final: 0.7769 (mmt90) REVERT: G 44 TYR cc_start: 0.6505 (m-80) cc_final: 0.5103 (m-80) REVERT: I 345 ASP cc_start: 0.7993 (t0) cc_final: 0.7676 (t0) REVERT: L 28 MET cc_start: 0.8724 (mmm) cc_final: 0.8139 (tpp) REVERT: L 143 ASP cc_start: 0.8716 (t70) cc_final: 0.8388 (t0) REVERT: L 145 PHE cc_start: 0.7144 (m-80) cc_final: 0.6209 (m-80) REVERT: L 147 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8299 (ptt90) REVERT: K 80 GLN cc_start: 0.7040 (tm-30) cc_final: 0.6553 (tm-30) REVERT: J 149 TRP cc_start: 0.4640 (OUTLIER) cc_final: 0.2750 (p-90) outliers start: 99 outliers final: 80 residues processed: 303 average time/residue: 0.3823 time to fit residues: 187.6029 Evaluate side-chains 289 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 204 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 70 ASN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 302 ILE Chi-restraints excluded: chain G residue 343 MET Chi-restraints excluded: chain G residue 367 TRP Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 266 ASP Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 147 ARG Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 149 TRP Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 56 CYS Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 228 optimal weight: 40.0000 chunk 305 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 264 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 287 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 295 optimal weight: 50.0000 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.054584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.043427 restraints weight = 238831.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.044356 restraints weight = 167697.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.044962 restraints weight = 123940.666| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 1.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.208 28849 Z= 0.383 Angle : 0.943 59.200 39099 Z= 0.495 Chirality : 0.051 1.116 4359 Planarity : 0.006 0.138 5118 Dihedral : 6.205 51.587 3961 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 42.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.35 % Rotamer: Outliers : 3.20 % Allowed : 25.90 % Favored : 70.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3638 helix: -0.06 (0.15), residues: 1179 sheet: -0.99 (0.18), residues: 762 loop : -1.55 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP I 215 HIS 0.016 0.002 HIS G 257 PHE 0.044 0.002 PHE B 230 TYR 0.037 0.003 TYR G 338 ARG 0.058 0.001 ARG B 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5554.68 seconds wall clock time: 103 minutes 51.45 seconds (6231.45 seconds total)