Starting phenix.real_space_refine on Thu Dec 14 11:45:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/12_2023/7ock_12809.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/12_2023/7ock_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_12809/12_2023/7ock_12809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/12_2023/7ock_12809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/12_2023/7ock_12809.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ock_12809/12_2023/7ock_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 15.02, per 1000 atoms: 0.53 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: 12.63 Conformation dependent library (CDL) restraints added in 5.1 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: 3.35 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: 11.13 Time building geometry restraints manager: 13.50 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: 1.310 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: 7.300 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 77.200 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.130 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.780 ------------------------------------------------------------------------------- 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 : 3.691 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 outliers start: 6 outliers final: 2 residues processed: 504 average time/residue: 0.4951 time to fit residues: 373.2045 Evaluate side-chains 272 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 3.333 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2502 time to fit residues: 5.7043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 10.0000 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: 5.9990 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 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 119 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4795 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28849 Z= 0.306 Angle : 0.782 12.325 39099 Z= 0.409 Chirality : 0.048 0.202 4359 Planarity : 0.006 0.123 5118 Dihedral : 5.793 33.707 3960 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 31.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 3.17 % Allowed : 16.32 % Favored : 80.51 % 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: -1.31 (0.13), residues: 3638 helix: -0.47 (0.14), residues: 1157 sheet: -0.11 (0.18), residues: 764 loop : -1.46 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 367 HIS 0.016 0.002 HIS D 14 PHE 0.025 0.003 PHE I 230 TYR 0.031 0.003 TYR D 351 ARG 0.018 0.001 ARG G 73 *********************** 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 409 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 314 time to evaluate : 3.494 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 outliers start: 95 outliers final: 53 residues processed: 391 average time/residue: 0.4622 time to fit residues: 280.5712 Evaluate side-chains 294 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 241 time to evaluate : 3.578 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 53 outliers final: 1 residues processed: 53 average time/residue: 0.3369 time to fit residues: 35.8325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 329 optimal weight: 10.0000 chunk 355 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 326 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 HIS ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS B 297 GLN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 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 ** 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 195 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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 HIS ** 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 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4991 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28849 Z= 0.250 Angle : 0.743 13.612 39099 Z= 0.380 Chirality : 0.046 0.250 4359 Planarity : 0.005 0.067 5118 Dihedral : 5.568 31.373 3960 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 31.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.14 % Favored : 94.72 % Rotamer: Outliers : 3.07 % Allowed : 18.09 % Favored : 78.84 % 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: -0.78 (0.14), residues: 3638 helix: 0.17 (0.15), residues: 1157 sheet: 0.14 (0.19), residues: 761 loop : -1.27 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 367 HIS 0.009 0.002 HIS D 14 PHE 0.028 0.002 PHE D 365 TYR 0.029 0.002 TYR D 351 ARG 0.007 0.001 ARG F 229 *********************** 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 355 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 263 time to evaluate : 3.359 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 outliers start: 92 outliers final: 32 residues processed: 337 average time/residue: 0.4419 time to fit residues: 238.4785 Evaluate side-chains 258 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 3.410 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3233 time to fit residues: 22.6471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 330 optimal weight: 0.4980 chunk 349 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 313 optimal weight: 0.4980 chunk 94 optimal weight: 9.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** 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 14 HIS ** E 79 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 119 GLN ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** G 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 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 171 GLN ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** 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 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 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28849 Z= 0.307 Angle : 0.811 16.231 39099 Z= 0.418 Chirality : 0.048 0.219 4359 Planarity : 0.006 0.108 5118 Dihedral : 5.818 30.222 3960 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 36.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.55 % Favored : 94.34 % Rotamer: Outliers : 3.44 % Allowed : 20.59 % Favored : 75.97 % 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: -1.06 (0.14), residues: 3638 helix: 0.01 (0.15), residues: 1164 sheet: -0.35 (0.18), residues: 803 loop : -1.34 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP F 367 HIS 0.012 0.002 HIS H 3 PHE 0.032 0.003 PHE D 365 TYR 0.045 0.003 TYR C 140 ARG 0.011 0.001 ARG J 86 *********************** 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 391 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 288 time to evaluate : 3.649 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 outliers start: 103 outliers final: 41 residues processed: 371 average time/residue: 0.4560 time to fit residues: 265.5330 Evaluate side-chains 274 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 233 time to evaluate : 3.499 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.3247 time to fit residues: 28.6202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 260 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 225 ASN B 297 GLN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 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 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 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 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** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 GLN I 195 GLN ** 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** ** K 128 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: 0.5557 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28849 Z= 0.281 Angle : 0.773 12.228 39099 Z= 0.396 Chirality : 0.046 0.201 4359 Planarity : 0.005 0.061 5118 Dihedral : 5.754 27.965 3960 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 35.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.31 % Favored : 94.58 % Rotamer: Outliers : 2.94 % Allowed : 22.03 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3638 helix: 0.09 (0.15), residues: 1175 sheet: -0.46 (0.18), residues: 788 loop : -1.27 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP I 215 HIS 0.011 0.002 HIS C 257 PHE 0.034 0.003 PHE D 365 TYR 0.043 0.003 TYR K 12 ARG 0.013 0.001 ARG C 256 *********************** 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 350 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 262 time to evaluate : 3.728 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 outliers start: 88 outliers final: 44 residues processed: 337 average time/residue: 0.4390 time to fit residues: 234.9116 Evaluate side-chains 270 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 226 time to evaluate : 3.555 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2904 time to fit residues: 27.9848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 1.9990 chunk 315 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 205 optimal weight: 0.3980 chunk 86 optimal weight: 0.0030 chunk 350 optimal weight: 10.0000 chunk 290 optimal weight: 30.0000 chunk 162 optimal weight: 0.0870 chunk 29 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 183 optimal weight: 0.0770 overall best weight: 0.1726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 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** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 189 HIS ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN G 195 GLN ** G 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** K 33 HIS ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28849 Z= 0.208 Angle : 0.722 12.678 39099 Z= 0.363 Chirality : 0.045 0.226 4359 Planarity : 0.005 0.053 5118 Dihedral : 5.422 34.703 3960 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 1.23 % Allowed : 23.33 % Favored : 75.43 % 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: -0.69 (0.14), residues: 3638 helix: 0.45 (0.15), residues: 1172 sheet: -0.28 (0.19), residues: 793 loop : -1.15 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 367 HIS 0.010 0.001 HIS K 33 PHE 0.031 0.002 PHE D 365 TYR 0.028 0.002 TYR E 357 ARG 0.016 0.001 ARG B 73 *********************** 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 295 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 258 time to evaluate : 3.368 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 outliers start: 37 outliers final: 16 residues processed: 283 average time/residue: 0.4457 time to fit residues: 199.9801 Evaluate side-chains 238 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 222 time to evaluate : 3.324 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3152 time to fit residues: 13.5681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 348 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN D 142 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 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 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 GLN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 21 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 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28849 Z= 0.284 Angle : 0.799 11.552 39099 Z= 0.411 Chirality : 0.048 0.323 4359 Planarity : 0.006 0.067 5118 Dihedral : 5.737 37.361 3960 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 38.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.10 % Favored : 93.79 % Rotamer: Outliers : 2.07 % Allowed : 23.46 % Favored : 74.47 % 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: -0.98 (0.14), residues: 3638 helix: 0.17 (0.15), residues: 1192 sheet: -0.62 (0.18), residues: 797 loop : -1.20 (0.16), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 367 HIS 0.017 0.002 HIS G 3 PHE 0.032 0.003 PHE K 127 TYR 0.036 0.003 TYR K 12 ARG 0.014 0.001 ARG E 147 *********************** 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 296 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 234 time to evaluate : 3.268 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 outliers start: 62 outliers final: 27 residues processed: 283 average time/residue: 0.4389 time to fit residues: 198.1452 Evaluate side-chains 240 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 3.519 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3107 time to fit residues: 19.4971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 274 optimal weight: 0.0770 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 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 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 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 195 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 257 HIS ** 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** I 171 GLN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS A 21 ASN K 33 HIS ** K 94 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.8171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28849 Z= 0.205 Angle : 0.742 15.916 39099 Z= 0.373 Chirality : 0.046 0.312 4359 Planarity : 0.005 0.057 5118 Dihedral : 5.518 36.500 3960 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 29.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 1.03 % Allowed : 24.20 % Favored : 74.77 % 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: -0.74 (0.14), residues: 3638 helix: 0.42 (0.15), residues: 1195 sheet: -0.45 (0.19), residues: 772 loop : -1.13 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 367 HIS 0.013 0.001 HIS L 105 PHE 0.034 0.002 PHE D 84 TYR 0.036 0.002 TYR L 12 ARG 0.015 0.001 ARG L 74 *********************** 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 265 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 3.554 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 outliers start: 31 outliers final: 15 residues processed: 258 average time/residue: 0.4511 time to fit residues: 184.0095 Evaluate side-chains 230 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 215 time to evaluate : 3.413 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3152 time to fit residues: 12.7684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 3.9990 chunk 334 optimal weight: 7.9990 chunk 304 optimal weight: 0.9980 chunk 325 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 255 optimal weight: 30.0000 chunk 99 optimal weight: 10.0000 chunk 293 optimal weight: 50.0000 chunk 307 optimal weight: 6.9990 chunk 324 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 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** ** C 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 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 103 ASN E 195 GLN ** E 225 ASN ** 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 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN I 21 GLN ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 171 GLN ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.9676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 28849 Z= 0.336 Angle : 0.886 14.942 39099 Z= 0.457 Chirality : 0.050 0.278 4359 Planarity : 0.007 0.150 5118 Dihedral : 6.177 31.315 3960 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 44.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.04 % Favored : 92.88 % Rotamer: Outliers : 0.97 % Allowed : 25.13 % Favored : 73.90 % 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: -1.37 (0.14), residues: 3638 helix: -0.13 (0.14), residues: 1196 sheet: -0.89 (0.18), residues: 765 loop : -1.43 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 159 HIS 0.014 0.002 HIS B 257 PHE 0.046 0.003 PHE C 333 TYR 0.029 0.003 TYR D 44 ARG 0.016 0.001 ARG L 74 *********************** 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 254 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 3.480 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 outliers start: 29 outliers final: 11 residues processed: 244 average time/residue: 0.4290 time to fit residues: 168.1855 Evaluate side-chains 215 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 3.203 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3003 time to fit residues: 10.0217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 8.9990 chunk 343 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 163 optimal weight: 0.0570 chunk 239 optimal weight: 20.0000 chunk 360 optimal weight: 6.9990 chunk 331 optimal weight: 0.3980 chunk 287 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 overall best weight: 3.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 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 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 119 GLN ** G 148 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 1.0100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28849 Z= 0.249 Angle : 0.810 13.978 39099 Z= 0.408 Chirality : 0.047 0.298 4359 Planarity : 0.005 0.083 5118 Dihedral : 5.886 39.192 3960 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 35.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.02 % Favored : 93.87 % Rotamer: Outliers : 0.43 % Allowed : 26.13 % Favored : 73.43 % 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: -1.17 (0.14), residues: 3638 helix: 0.15 (0.15), residues: 1180 sheet: -0.81 (0.19), residues: 748 loop : -1.37 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 367 HIS 0.016 0.002 HIS L 105 PHE 0.060 0.003 PHE L 11 TYR 0.047 0.002 TYR A 12 ARG 0.021 0.001 ARG L 74 ********************** 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 238 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 225 time to evaluate : 3.629 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 outliers start: 13 outliers final: 8 residues processed: 233 average time/residue: 0.4535 time to fit residues: 170.6553 Evaluate side-chains 216 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 208 time to evaluate : 3.485 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2873 time to fit residues: 8.9717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 87 optimal weight: 4.9990 chunk 264 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 287 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 295 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** 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 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** E 225 ASN ** 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** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 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 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.054729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.043771 restraints weight = 235739.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.044698 restraints weight = 167538.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.045347 restraints weight = 122892.063| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 1.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 28849 Z= 0.303 Angle : 0.837 13.835 39099 Z= 0.426 Chirality : 0.049 0.371 4359 Planarity : 0.006 0.058 5118 Dihedral : 6.039 36.554 3960 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 39.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.53 % Favored : 92.39 % Rotamer: Outliers : 0.30 % Allowed : 26.54 % Favored : 73.16 % 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: -1.36 (0.14), residues: 3638 helix: 0.01 (0.14), residues: 1174 sheet: -1.00 (0.18), residues: 767 loop : -1.46 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP E 367 HIS 0.012 0.002 HIS C 348 PHE 0.041 0.003 PHE L 11 TYR 0.034 0.003 TYR C 280 ARG 0.015 0.001 ARG E 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5651.15 seconds wall clock time: 105 minutes 51.61 seconds (6351.61 seconds total)