Starting phenix.real_space_refine on Fri Feb 23 10:51:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwy_27767/02_2024/8dwy_27767.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwy_27767/02_2024/8dwy_27767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwy_27767/02_2024/8dwy_27767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwy_27767/02_2024/8dwy_27767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwy_27767/02_2024/8dwy_27767.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwy_27767/02_2024/8dwy_27767.pdb" } resolution = 3.18 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= 0.006 sd= 0.049 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 260 5.16 5 C 24016 2.51 5 N 6528 2.21 5 O 7244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B ASP 343": "OD1" <-> "OD2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "C TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 385": "OD1" <-> "OD2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D ASP 284": "OD1" <-> "OD2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D ASP 343": "OD1" <-> "OD2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D ASP 385": "OD1" <-> "OD2" Residue "D ASP 401": "OD1" <-> "OD2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 63": "OD1" <-> "OD2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M ASP 174": "OD1" <-> "OD2" Residue "M TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 247": "OE1" <-> "OE2" Residue "M TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 59": "OD1" <-> "OD2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 214": "OD1" <-> "OD2" Residue "N GLU 247": "OE1" <-> "OE2" Residue "N ASP 290": "OD1" <-> "OD2" Residue "N TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 303": "OE1" <-> "OE2" Residue "N GLU 308": "OE1" <-> "OE2" Residue "N GLU 354": "OE1" <-> "OE2" Residue "N TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 43": "OD1" <-> "OD2" Residue "O ASP 59": "OD1" <-> "OD2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O ASP 63": "OD1" <-> "OD2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O GLU 109": "OE1" <-> "OE2" Residue "O GLU 132": "OE1" <-> "OE2" Residue "O GLU 150": "OE1" <-> "OE2" Residue "O ASP 177": "OD1" <-> "OD2" Residue "O GLU 208": "OE1" <-> "OE2" Residue "O ASP 214": "OD1" <-> "OD2" Residue "O ASP 223": "OD1" <-> "OD2" Residue "O GLU 303": "OE1" <-> "OE2" Residue "O TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 21": "OD1" <-> "OD2" Residue "P GLU 24": "OE1" <-> "OE2" Residue "P ASP 43": "OD1" <-> "OD2" Residue "P ASP 63": "OD1" <-> "OD2" Residue "P GLU 79": "OE1" <-> "OE2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "P ASP 174": "OD1" <-> "OD2" Residue "P ASP 223": "OD1" <-> "OD2" Residue "P ASP 290": "OD1" <-> "OD2" Residue "P TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 309": "OE1" <-> "OE2" Residue "P TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 260": "OE1" <-> "OE2" Residue "R GLU 163": "OE1" <-> "OE2" Residue "T TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 181": "OE1" <-> "OE2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38048 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "M" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "N" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "O" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "P" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "Q" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "R" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "S" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "T" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "H" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "V" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "U" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "X" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "W" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "Z" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "Y" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 20.06, per 1000 atoms: 0.53 Number of scatterers: 38048 At special positions: 0 Unit cell: (169.36, 245.92, 238.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 260 16.00 O 7244 8.00 N 6528 7.00 C 24016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=68, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 125 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 28 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 105 " distance=2.03 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 266 " distance=2.06 Simple disulfide: pdb=" SG CYS M 201 " - pdb=" SG CYS M 225 " distance=2.03 Simple disulfide: pdb=" SG CYS M 203 " - pdb=" SG CYS M 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 396 " - pdb=" SG CYS M 417 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 125 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 28 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 105 " distance=2.03 Simple disulfide: pdb=" SG CYS N 153 " - pdb=" SG CYS N 266 " distance=2.04 Simple disulfide: pdb=" SG CYS N 201 " - pdb=" SG CYS N 225 " distance=2.03 Simple disulfide: pdb=" SG CYS N 203 " - pdb=" SG CYS N 220 " distance=2.03 Simple disulfide: pdb=" SG CYS N 396 " - pdb=" SG CYS N 417 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 125 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 28 " distance=2.03 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 105 " distance=2.03 Simple disulfide: pdb=" SG CYS O 153 " - pdb=" SG CYS O 266 " distance=2.04 Simple disulfide: pdb=" SG CYS O 201 " - pdb=" SG CYS O 225 " distance=2.03 Simple disulfide: pdb=" SG CYS O 203 " - pdb=" SG CYS O 220 " distance=2.03 Simple disulfide: pdb=" SG CYS O 396 " - pdb=" SG CYS O 417 " distance=2.04 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 125 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 28 " distance=2.03 Simple disulfide: pdb=" SG CYS P 91 " - pdb=" SG CYS P 105 " distance=2.03 Simple disulfide: pdb=" SG CYS P 153 " - pdb=" SG CYS P 266 " distance=2.04 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 225 " distance=2.03 Simple disulfide: pdb=" SG CYS P 203 " - pdb=" SG CYS P 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 396 " - pdb=" SG CYS P 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 90 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 90 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 141 " " NAG B 501 " - " ASN B 141 " " NAG C 501 " - " ASN C 141 " " NAG D 501 " - " ASN D 141 " " NAG M 501 " - " ASN M 263 " " NAG M 502 " - " ASN M 345 " " NAG N 501 " - " ASN N 263 " " NAG N 502 " - " ASN N 345 " " NAG O 501 " - " ASN O 263 " " NAG O 502 " - " ASN O 345 " " NAG P 501 " - " ASN P 263 " " NAG P 502 " - " ASN P 345 " Time building additional restraints: 12.72 Conformation dependent library (CDL) restraints added in 6.9 seconds 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9104 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 111 sheets defined 13.3% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.89 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.658A pdb=" N LYS A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.850A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.760A pdb=" N ALA A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 287 " --> pdb=" O ASP A 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 287' Processing helix chain 'A' and resid 403 through 439 removed outlier: 3.569A pdb=" N LYS A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.517A pdb=" N LYS B 115 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.904A pdb=" N TYR B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 246 " --> pdb=" O TYR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.680A pdb=" N ALA B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 287 " --> pdb=" O ASP B 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 283 through 287' Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 403 through 439 removed outlier: 3.660A pdb=" N TRP B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.720A pdb=" N LYS C 115 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 removed outlier: 4.179A pdb=" N TYR C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.501A pdb=" N HIS C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 4.242A pdb=" N GLY C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.602A pdb=" N ALA C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'C' and resid 403 through 439 removed outlier: 3.633A pdb=" N TRP C 409 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 427 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.700A pdb=" N LYS D 115 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.997A pdb=" N TYR D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 246 " --> pdb=" O TYR D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 removed outlier: 3.712A pdb=" N ALA D 286 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 287 " --> pdb=" O ASP D 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 283 through 287' Processing helix chain 'D' and resid 403 through 439 removed outlier: 3.626A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 427 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 10 removed outlier: 3.591A pdb=" N LYS M 10 " --> pdb=" O ASN M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 363 removed outlier: 3.576A pdb=" N ILE M 356 " --> pdb=" O PRO M 352 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU M 357 " --> pdb=" O HIS M 353 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU M 362 " --> pdb=" O TYR M 358 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 398 removed outlier: 3.800A pdb=" N VAL M 368 " --> pdb=" O PRO M 364 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL M 369 " --> pdb=" O THR M 365 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG M 394 " --> pdb=" O VAL M 390 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG M 395 " --> pdb=" O CYS M 391 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 402 Processing helix chain 'M' and resid 409 through 415 Processing helix chain 'N' and resid 6 through 10 removed outlier: 3.540A pdb=" N LYS N 10 " --> pdb=" O ASN N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 83 No H-bonds generated for 'chain 'N' and resid 81 through 83' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.537A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU N 362 " --> pdb=" O TYR N 358 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 403 removed outlier: 3.621A pdb=" N VAL N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA N 385 " --> pdb=" O MET N 381 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS N 389 " --> pdb=" O ALA N 385 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG N 394 " --> pdb=" O VAL N 390 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG N 395 " --> pdb=" O CYS N 391 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 4.022A pdb=" N THR N 403 " --> pdb=" O PRO N 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 Processing helix chain 'O' and resid 6 through 10 removed outlier: 3.632A pdb=" N LYS O 10 " --> pdb=" O ASN O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 83 No H-bonds generated for 'chain 'O' and resid 81 through 83' Processing helix chain 'O' and resid 351 through 363 removed outlier: 3.615A pdb=" N ILE O 355 " --> pdb=" O HIS O 351 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE O 356 " --> pdb=" O PRO O 352 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU O 357 " --> pdb=" O HIS O 353 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU O 361 " --> pdb=" O LEU O 357 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU O 362 " --> pdb=" O TYR O 358 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 398 removed outlier: 3.617A pdb=" N VAL O 368 " --> pdb=" O PRO O 364 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL O 369 " --> pdb=" O THR O 365 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG O 395 " --> pdb=" O CYS O 391 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 403 removed outlier: 3.549A pdb=" N LEU O 402 " --> pdb=" O THR O 398 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR O 403 " --> pdb=" O PRO O 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 398 through 403' Processing helix chain 'O' and resid 409 through 415 Processing helix chain 'P' and resid 6 through 10 removed outlier: 3.603A pdb=" N LYS P 10 " --> pdb=" O ASN P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'P' and resid 351 through 361 removed outlier: 3.754A pdb=" N LEU P 357 " --> pdb=" O HIS P 353 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR P 358 " --> pdb=" O GLU P 354 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR P 359 " --> pdb=" O ILE P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 403 removed outlier: 3.910A pdb=" N VAL P 368 " --> pdb=" O PRO P 364 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL P 369 " --> pdb=" O THR P 365 " (cutoff:3.500A) Proline residue: P 399 - end of helix removed outlier: 3.629A pdb=" N LEU P 402 " --> pdb=" O THR P 398 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR P 403 " --> pdb=" O PRO P 399 " (cutoff:3.500A) Processing helix chain 'P' and resid 409 through 415 Processing helix chain 'Q' and resid 148 through 152 Processing helix chain 'Q' and resid 168 through 175 removed outlier: 3.577A pdb=" N MET Q 171 " --> pdb=" O PRO Q 168 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER Q 173 " --> pdb=" O HIS Q 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 152 Processing helix chain 'R' and resid 168 through 175 removed outlier: 4.909A pdb=" N SER R 173 " --> pdb=" O HIS R 170 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP R 174 " --> pdb=" O MET R 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 148 through 152 removed outlier: 3.774A pdb=" N LYS S 151 " --> pdb=" O ASP S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 175 removed outlier: 3.661A pdb=" N MET S 171 " --> pdb=" O PRO S 168 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER S 173 " --> pdb=" O HIS S 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 148 through 152 Processing helix chain 'T' and resid 171 through 175 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.533A pdb=" N GLU H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.674A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.888A pdb=" N THR H 91 " --> pdb=" O ASN H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'V' and resid 28 through 32 removed outlier: 3.553A pdb=" N GLU V 31 " --> pdb=" O THR V 28 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR V 32 " --> pdb=" O PHE V 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 28 through 32' Processing helix chain 'V' and resid 62 through 65 removed outlier: 3.580A pdb=" N LYS V 65 " --> pdb=" O GLU V 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 62 through 65' Processing helix chain 'V' and resid 87 through 91 removed outlier: 3.956A pdb=" N THR V 91 " --> pdb=" O ASN V 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 34 removed outlier: 3.961A pdb=" N CYS U 34 " --> pdb=" O SER U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 85 Processing helix chain 'X' and resid 28 through 32 removed outlier: 3.542A pdb=" N GLU X 31 " --> pdb=" O THR X 28 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR X 32 " --> pdb=" O PHE X 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 28 through 32' Processing helix chain 'X' and resid 62 through 65 removed outlier: 3.656A pdb=" N LYS X 65 " --> pdb=" O GLU X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 62 through 65' Processing helix chain 'X' and resid 87 through 91 removed outlier: 3.976A pdb=" N THR X 91 " --> pdb=" O ASN X 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 85 Processing helix chain 'Z' and resid 28 through 32 removed outlier: 3.549A pdb=" N GLU Z 31 " --> pdb=" O THR Z 28 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR Z 32 " --> pdb=" O PHE Z 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 28 through 32' Processing helix chain 'Z' and resid 62 through 65 removed outlier: 3.605A pdb=" N LYS Z 65 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 62 through 65' Processing helix chain 'Z' and resid 87 through 91 removed outlier: 3.977A pdb=" N THR Z 91 " --> pdb=" O ASN Z 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 34 removed outlier: 4.039A pdb=" N CYS Y 34 " --> pdb=" O SER Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 4.005A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS A 132 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 146 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 3.506A pdb=" N ALA A 262 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 48 removed outlier: 7.232A pdb=" N ALA A 121 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 177 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.618A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.618A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 104 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 79 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 106 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 77 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.507A pdb=" N GLY A 91 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA9, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AB1, first strand: chain 'A' and resid 300 through 306 removed outlier: 3.702A pdb=" N SER A 300 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL A 315 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 356 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 350 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.518A pdb=" N VAL A 346 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 326 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.730A pdb=" N TYR M 297 " --> pdb=" O HIS M 307 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS M 307 " --> pdb=" O TYR M 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.707A pdb=" N LYS B 160 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 19 removed outlier: 4.124A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS B 132 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AB7, first strand: chain 'B' and resid 42 through 48 removed outlier: 7.125A pdb=" N ALA B 121 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 177 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.505A pdb=" N TYR B 59 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.511A pdb=" N LYS B 79 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 106 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AC3, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AC4, first strand: chain 'B' and resid 300 through 306 removed outlier: 3.651A pdb=" N SER B 300 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 356 " --> pdb=" O GLY B 314 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 350 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 343 through 346 removed outlier: 3.606A pdb=" N GLY B 326 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 387 through 388 removed outlier: 3.576A pdb=" N TYR N 297 " --> pdb=" O HIS N 307 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS N 307 " --> pdb=" O TYR N 297 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.705A pdb=" N LYS C 160 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 15 through 19 removed outlier: 4.263A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS C 132 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER C 130 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 38 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 146 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AD1, first strand: chain 'C' and resid 42 through 48 removed outlier: 7.106A pdb=" N ALA C 121 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE C 47 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA C 119 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 177 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.642A pdb=" N LYS C 52 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.642A pdb=" N LYS C 52 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 104 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 79 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 106 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 77 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD5, first strand: chain 'C' and resid 219 through 221 Processing sheet with id=AD6, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.589A pdb=" N SER C 300 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 319 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL C 315 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 343 through 346 removed outlier: 3.523A pdb=" N GLY C 326 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AD9, first strand: chain 'C' and resid 387 through 388 removed outlier: 3.720A pdb=" N TYR O 297 " --> pdb=" O HIS O 307 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS O 307 " --> pdb=" O TYR O 297 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.724A pdb=" N LYS D 160 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 15 through 19 removed outlier: 9.689A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N MET D 31 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL D 135 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 33 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA D 131 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR D 37 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA D 129 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU D 39 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA D 127 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 120 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE D 177 " --> pdb=" O TYR D 122 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.775A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA D 127 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU D 39 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA D 129 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR D 37 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA D 131 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 33 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL D 135 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N MET D 31 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.666A pdb=" N LYS D 52 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.666A pdb=" N LYS D 52 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 104 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS D 79 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 106 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 77 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AE7, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AE8, first strand: chain 'D' and resid 296 through 306 removed outlier: 6.600A pdb=" N THR D 321 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET D 299 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS D 319 " --> pdb=" O MET D 299 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS D 301 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE D 317 " --> pdb=" O CYS D 301 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL D 303 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL D 315 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 350 " --> pdb=" O TYR D 320 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 343 through 346 removed outlier: 3.606A pdb=" N GLY D 326 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 337 through 339 Processing sheet with id=AF2, first strand: chain 'D' and resid 387 through 388 removed outlier: 3.717A pdb=" N TYR P 297 " --> pdb=" O HIS P 307 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 17 through 19 removed outlier: 3.708A pdb=" N ALA M 17 " --> pdb=" O SER M 30 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 34 through 38 removed outlier: 5.095A pdb=" N GLN M 49 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE M 37 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS M 47 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 27.130A pdb=" N LYS M 47 " --> pdb=" O ASP M 71 " (cutoff:3.500A) removed outlier: 23.791A pdb=" N ASP M 71 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 17.636A pdb=" N GLN M 49 " --> pdb=" O TYR M 69 " (cutoff:3.500A) removed outlier: 14.624A pdb=" N TYR M 69 " --> pdb=" O GLN M 49 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N SER M 51 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU M 67 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N GLN M 53 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N THR M 65 " --> pdb=" O GLN M 53 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY M 55 " --> pdb=" O ASP M 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR M 74 " --> pdb=" O ASP M 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 34 through 38 removed outlier: 5.095A pdb=" N GLN M 49 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE M 37 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS M 47 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA M 103 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS M 99 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N LEU M 52 " --> pdb=" O MET M 97 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N MET M 97 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N ILE M 54 " --> pdb=" O GLY M 95 " (cutoff:3.500A) removed outlier: 11.242A pdb=" N GLY M 95 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 16.815A pdb=" N ILE M 56 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 19.656A pdb=" N ILE M 93 " --> pdb=" O ILE M 56 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 84 through 86 removed outlier: 4.345A pdb=" N GLU M 109 " --> pdb=" O PHE M 129 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 149 through 156 removed outlier: 3.650A pdb=" N CYS M 153 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR M 155 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA M 262 " --> pdb=" O THR M 155 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 236 through 237 removed outlier: 3.889A pdb=" N GLY M 253 " --> pdb=" O VAL M 169 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 181 through 184 removed outlier: 3.813A pdb=" N LYS M 189 " --> pdb=" O THR M 182 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS M 215 " --> pdb=" O ILE M 190 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 207 through 211 removed outlier: 3.886A pdb=" N GLY M 209 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR M 199 " --> pdb=" O GLY M 209 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL M 197 " --> pdb=" O THR M 211 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 275 through 279 removed outlier: 3.852A pdb=" N GLN M 282 " --> pdb=" O GLY M 279 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS M 315 " --> pdb=" O LEU M 287 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.598A pdb=" N ALA N 17 " --> pdb=" O SER N 30 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 37 through 38 removed outlier: 3.564A pdb=" N LYS N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 17.588A pdb=" N GLN N 49 " --> pdb=" O TYR N 69 " (cutoff:3.500A) removed outlier: 14.576A pdb=" N TYR N 69 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 12.467A pdb=" N SER N 51 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N LEU N 67 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 12.104A pdb=" N GLN N 53 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N THR N 65 " --> pdb=" O GLN N 53 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY N 55 " --> pdb=" O ASP N 63 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 37 through 38 removed outlier: 3.564A pdb=" N LYS N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS N 99 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N LEU N 52 " --> pdb=" O MET N 97 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N MET N 97 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N ILE N 54 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 11.423A pdb=" N GLY N 95 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 16.958A pdb=" N ILE N 56 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 19.798A pdb=" N ILE N 93 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 84 through 86 removed outlier: 4.405A pdb=" N GLU N 109 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE N 129 " --> pdb=" O GLU N 109 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 149 through 156 Processing sheet with id=AG8, first strand: chain 'N' and resid 236 through 237 removed outlier: 3.509A pdb=" N VAL N 169 " --> pdb=" O GLY N 253 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY N 253 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 175 through 176 removed outlier: 3.765A pdb=" N GLY N 209 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN N 207 " --> pdb=" O CYS N 201 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 182 through 184 removed outlier: 3.523A pdb=" N ASN N 187 " --> pdb=" O GLN N 184 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS N 215 " --> pdb=" O ILE N 190 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 275 through 279 removed outlier: 3.780A pdb=" N GLN N 282 " --> pdb=" O GLY N 279 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS N 315 " --> pdb=" O LEU N 287 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 17 through 19 removed outlier: 3.647A pdb=" N ALA O 17 " --> pdb=" O SER O 30 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 34 through 38 removed outlier: 8.892A pdb=" N LEU O 34 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER O 51 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG O 36 " --> pdb=" O GLN O 49 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN O 49 " --> pdb=" O ARG O 36 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N SER O 51 " --> pdb=" O MET O 70 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET O 70 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN O 53 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS O 66 " --> pdb=" O GLY O 55 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 34 through 38 removed outlier: 8.892A pdb=" N LEU O 34 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER O 51 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG O 36 " --> pdb=" O GLN O 49 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN O 49 " --> pdb=" O ARG O 36 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA O 103 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS O 99 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N LEU O 52 " --> pdb=" O MET O 97 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N MET O 97 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N ILE O 54 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N GLY O 95 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 17.322A pdb=" N ILE O 56 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 19.994A pdb=" N ILE O 93 " --> pdb=" O ILE O 56 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 84 through 86 removed outlier: 3.535A pdb=" N GLY O 114 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU O 109 " --> pdb=" O PHE O 129 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 149 through 156 removed outlier: 3.651A pdb=" N THR O 155 " --> pdb=" O ALA O 262 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA O 262 " --> pdb=" O THR O 155 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 236 through 237 removed outlier: 4.178A pdb=" N GLY O 253 " --> pdb=" O VAL O 169 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 175 through 176 removed outlier: 3.699A pdb=" N GLY O 209 " --> pdb=" O TYR O 199 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN O 207 " --> pdb=" O CYS O 201 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 181 through 184 removed outlier: 3.569A pdb=" N ASN O 187 " --> pdb=" O GLN O 184 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS O 215 " --> pdb=" O ILE O 190 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 275 through 279 removed outlier: 3.865A pdb=" N LYS O 315 " --> pdb=" O LEU O 287 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'P' and resid 17 through 19 removed outlier: 3.639A pdb=" N CYS P 28 " --> pdb=" O CYS P 19 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 74 through 79 removed outlier: 3.607A pdb=" N THR P 74 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY P 55 " --> pdb=" O ASP P 63 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N THR P 65 " --> pdb=" O GLN P 53 " (cutoff:3.500A) removed outlier: 12.017A pdb=" N GLN P 53 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 11.660A pdb=" N LEU P 67 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N SER P 51 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 14.479A pdb=" N TYR P 69 " --> pdb=" O GLN P 49 " (cutoff:3.500A) removed outlier: 17.643A pdb=" N GLN P 49 " --> pdb=" O TYR P 69 " (cutoff:3.500A) removed outlier: 23.972A pdb=" N ASP P 71 " --> pdb=" O LYS P 47 " (cutoff:3.500A) removed outlier: 27.267A pdb=" N LYS P 47 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N HIS P 99 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N LEU P 52 " --> pdb=" O MET P 97 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N MET P 97 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N ILE P 54 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 11.373A pdb=" N GLY P 95 " --> pdb=" O ILE P 54 " (cutoff:3.500A) removed outlier: 17.200A pdb=" N ILE P 56 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 19.984A pdb=" N ILE P 93 " --> pdb=" O ILE P 56 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 84 through 86 removed outlier: 4.261A pdb=" N GLU P 109 " --> pdb=" O PHE P 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE P 115 " --> pdb=" O HIS P 123 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'P' and resid 149 through 156 removed outlier: 3.640A pdb=" N VAL P 264 " --> pdb=" O CYS P 153 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR P 155 " --> pdb=" O ALA P 262 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P' and resid 236 through 237 removed outlier: 3.957A pdb=" N GLY P 253 " --> pdb=" O VAL P 169 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'P' and resid 175 through 176 removed outlier: 3.531A pdb=" N THR P 175 " --> pdb=" O VAL P 229 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR P 199 " --> pdb=" O GLY P 209 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY P 209 " --> pdb=" O TYR P 199 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 181 through 184 removed outlier: 3.871A pdb=" N LYS P 215 " --> pdb=" O ILE P 190 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'P' and resid 275 through 279 removed outlier: 3.734A pdb=" N GLN P 282 " --> pdb=" O GLY P 279 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS P 315 " --> pdb=" O LEU P 287 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Q' and resid 143 through 144 removed outlier: 6.539A pdb=" N PHE Q 115 " --> pdb=" O TYR Q 126 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR Q 126 " --> pdb=" O PHE Q 115 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL Q 117 " --> pdb=" O MET Q 124 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR Q 126 " --> pdb=" O PRO Q 137 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU Q 162 " --> pdb=" O SER Q 157 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER Q 157 " --> pdb=" O LEU Q 162 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS Q 164 " --> pdb=" O LYS Q 155 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS Q 155 " --> pdb=" O CYS Q 164 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Q' and resid 249 through 253 removed outlier: 3.883A pdb=" N ILE Q 249 " --> pdb=" O ASN Q 246 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN Q 246 " --> pdb=" O ILE Q 249 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA Q 239 " --> pdb=" O GLY Q 231 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY Q 231 " --> pdb=" O ALA Q 239 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER Q 241 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP Q 245 " --> pdb=" O VAL Q 225 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N VAL Q 225 " --> pdb=" O TRP Q 245 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE Q 217 " --> pdb=" O VAL Q 225 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY Q 185 " --> pdb=" O TYR Q 196 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR Q 196 " --> pdb=" O GLY Q 185 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ALA Q 193 " --> pdb=" O PRO Q 204 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG Q 200 " --> pdb=" O SER Q 197 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE Q 201 " --> pdb=" O LEU Q 240 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU Q 240 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 143 through 144 removed outlier: 4.159A pdb=" N GLY R 125 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N HIS R 119 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL R 123 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TYR R 126 " --> pdb=" O PRO R 137 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA R 165 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU R 162 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS R 164 " --> pdb=" O LYS R 155 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 177 through 178 removed outlier: 7.119A pdb=" N LYS R 177 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA R 226 " --> pdb=" O LYS R 177 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE R 217 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY R 185 " --> pdb=" O TYR R 196 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY R 192 " --> pdb=" O TRP R 189 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA R 193 " --> pdb=" O PRO R 204 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE R 201 " --> pdb=" O LEU R 240 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE R 249 " --> pdb=" O ASN R 246 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 177 through 178 removed outlier: 7.119A pdb=" N LYS R 177 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA R 226 " --> pdb=" O LYS R 177 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N VAL R 225 " --> pdb=" O TRP R 245 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP R 245 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER R 241 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY R 231 " --> pdb=" O ALA R 239 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA R 239 " --> pdb=" O GLY R 231 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE R 249 " --> pdb=" O ASN R 246 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 143 through 144 removed outlier: 6.910A pdb=" N PHE S 115 " --> pdb=" O TYR S 126 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR S 126 " --> pdb=" O PHE S 115 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL S 117 " --> pdb=" O MET S 124 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR S 126 " --> pdb=" O PRO S 137 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU S 162 " --> pdb=" O SER S 157 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER S 157 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS S 164 " --> pdb=" O LYS S 155 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS S 155 " --> pdb=" O CYS S 164 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 249 through 253 removed outlier: 3.523A pdb=" N ILE S 249 " --> pdb=" O ASN S 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER S 241 " --> pdb=" O GLY S 230 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY S 230 " --> pdb=" O SER S 241 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL S 243 " --> pdb=" O VAL S 228 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL S 228 " --> pdb=" O VAL S 243 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N TRP S 245 " --> pdb=" O ALA S 226 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA S 226 " --> pdb=" O TRP S 245 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE S 217 " --> pdb=" O VAL S 225 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY S 185 " --> pdb=" O TYR S 196 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR S 196 " --> pdb=" O GLY S 185 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ALA S 193 " --> pdb=" O PRO S 204 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE S 201 " --> pdb=" O LEU S 240 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'T' and resid 143 through 144 removed outlier: 6.837A pdb=" N PHE T 115 " --> pdb=" O TYR T 126 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR T 126 " --> pdb=" O PHE T 115 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL T 117 " --> pdb=" O MET T 124 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR T 126 " --> pdb=" O PRO T 137 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS T 128 " --> pdb=" O MET T 135 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU T 162 " --> pdb=" O SER T 157 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER T 157 " --> pdb=" O LEU T 162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS T 164 " --> pdb=" O LYS T 155 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'T' and resid 250 through 253 removed outlier: 4.395A pdb=" N GLY T 230 " --> pdb=" O SER T 241 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL T 243 " --> pdb=" O VAL T 228 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL T 228 " --> pdb=" O VAL T 243 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TRP T 245 " --> pdb=" O ALA T 226 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA T 226 " --> pdb=" O TRP T 245 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE T 217 " --> pdb=" O VAL T 225 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN T 188 " --> pdb=" O PHE T 218 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ALA T 193 " --> pdb=" O PRO T 204 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE T 201 " --> pdb=" O LEU T 240 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.726A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.775A pdb=" N GLU H 10 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 114 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.633A pdb=" N ARG L 23 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.686A pdb=" N ILE L 87 " --> pdb=" O GLU L 40 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AK7, first strand: chain 'V' and resid 3 through 6 removed outlier: 3.603A pdb=" N SER V 71 " --> pdb=" O TYR V 80 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'V' and resid 10 through 12 removed outlier: 3.656A pdb=" N GLU V 10 " --> pdb=" O THR V 112 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET V 34 " --> pdb=" O LEU V 50 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU V 50 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TRP V 36 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET V 48 " --> pdb=" O TRP V 36 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'U' and resid 4 through 6 removed outlier: 3.530A pdb=" N ARG U 23 " --> pdb=" O THR U 5 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'U' and resid 9 through 12 removed outlier: 3.609A pdb=" N ILE U 87 " --> pdb=" O GLU U 40 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP U 37 " --> pdb=" O LEU U 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE U 45 " --> pdb=" O LYS U 41 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'U' and resid 9 through 12 Processing sheet with id=AL3, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.720A pdb=" N SER X 71 " --> pdb=" O TYR X 80 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.587A pdb=" N GLU X 10 " --> pdb=" O THR X 112 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N MET X 34 " --> pdb=" O LEU X 50 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TRP X 36 " --> pdb=" O MET X 48 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET X 48 " --> pdb=" O TRP X 36 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'W' and resid 4 through 6 Processing sheet with id=AL6, first strand: chain 'W' and resid 9 through 12 removed outlier: 3.689A pdb=" N ILE W 87 " --> pdb=" O GLU W 40 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP W 37 " --> pdb=" O LEU W 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE W 45 " --> pdb=" O LYS W 41 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'W' and resid 9 through 12 Processing sheet with id=AL8, first strand: chain 'Z' and resid 3 through 6 removed outlier: 3.697A pdb=" N SER Z 71 " --> pdb=" O TYR Z 80 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'Z' and resid 10 through 12 removed outlier: 3.581A pdb=" N GLU Z 10 " --> pdb=" O THR Z 112 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N MET Z 34 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU Z 50 " --> pdb=" O MET Z 34 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TRP Z 36 " --> pdb=" O MET Z 48 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET Z 48 " --> pdb=" O TRP Z 36 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'Y' and resid 4 through 6 Processing sheet with id=AM2, first strand: chain 'Y' and resid 9 through 12 removed outlier: 3.625A pdb=" N ILE Y 87 " --> pdb=" O GLU Y 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP Y 37 " --> pdb=" O LEU Y 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE Y 45 " --> pdb=" O LYS Y 41 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'Y' and resid 9 through 12 1387 hydrogen bonds defined for protein. 3513 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: 16.12 Time building geometry restraints manager: 13.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12444 1.35 - 1.48: 9895 1.48 - 1.61: 16305 1.61 - 1.74: 0 1.74 - 1.86: 352 Bond restraints: 38996 Sorted by residual: bond pdb=" CB CYS O 266 " pdb=" SG CYS O 266 " ideal model delta sigma weight residual 1.808 1.863 -0.055 3.30e-02 9.18e+02 2.73e+00 bond pdb=" CB PRO P 240 " pdb=" CG PRO P 240 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.33e+00 bond pdb=" CB CYS M 266 " pdb=" SG CYS M 266 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.27e+00 bond pdb=" C1 NAG N 501 " pdb=" O5 NAG N 501 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C1 NAG N 502 " pdb=" O5 NAG N 502 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 ... (remaining 38991 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.20: 1293 106.20 - 113.19: 21311 113.19 - 120.18: 12648 120.18 - 127.17: 17432 127.17 - 134.16: 456 Bond angle restraints: 53140 Sorted by residual: angle pdb=" CA PRO P 240 " pdb=" N PRO P 240 " pdb=" CD PRO P 240 " ideal model delta sigma weight residual 112.00 103.27 8.73 1.40e+00 5.10e-01 3.89e+01 angle pdb=" C CYS M 266 " pdb=" CA CYS M 266 " pdb=" CB CYS M 266 " ideal model delta sigma weight residual 109.79 119.85 -10.06 2.05e+00 2.38e-01 2.41e+01 angle pdb=" CA GLU N 401 " pdb=" CB GLU N 401 " pdb=" CG GLU N 401 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" N CYS M 266 " pdb=" CA CYS M 266 " pdb=" CB CYS M 266 " ideal model delta sigma weight residual 111.55 104.47 7.08 1.74e+00 3.30e-01 1.66e+01 angle pdb=" CA LEU Q 229 " pdb=" CB LEU Q 229 " pdb=" CG LEU Q 229 " ideal model delta sigma weight residual 116.30 130.21 -13.91 3.50e+00 8.16e-02 1.58e+01 ... (remaining 53135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21524 17.90 - 35.80: 1535 35.80 - 53.70: 352 53.70 - 71.60: 57 71.60 - 89.51: 24 Dihedral angle restraints: 23492 sinusoidal: 9280 harmonic: 14212 Sorted by residual: dihedral pdb=" CB CYS M 153 " pdb=" SG CYS M 153 " pdb=" SG CYS M 266 " pdb=" CB CYS M 266 " ideal model delta sinusoidal sigma weight residual 93.00 165.58 -72.58 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS N 153 " pdb=" SG CYS N 153 " pdb=" SG CYS N 266 " pdb=" CB CYS N 266 " ideal model delta sinusoidal sigma weight residual -86.00 -153.90 67.90 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CB CYS D 68 " pdb=" SG CYS D 68 " pdb=" SG CYS D 78 " pdb=" CB CYS D 78 " ideal model delta sinusoidal sigma weight residual -86.00 -146.53 60.53 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 23489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 5788 0.109 - 0.217: 231 0.217 - 0.326: 6 0.326 - 0.434: 2 0.434 - 0.543: 1 Chirality restraints: 6028 Sorted by residual: chirality pdb=" C1 NAG P 501 " pdb=" ND2 ASN P 263 " pdb=" C2 NAG P 501 " pdb=" O5 NAG P 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C1 NAG N 501 " pdb=" ND2 ASN N 263 " pdb=" C2 NAG N 501 " pdb=" O5 NAG N 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C1 NAG M 501 " pdb=" ND2 ASN M 263 " pdb=" C2 NAG M 501 " pdb=" O5 NAG M 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 6025 not shown) Planarity restraints: 6840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER P 239 " -0.125 5.00e-02 4.00e+02 1.84e-01 5.43e+01 pdb=" N PRO P 240 " 0.318 5.00e-02 4.00e+02 pdb=" CA PRO P 240 " -0.105 5.00e-02 4.00e+02 pdb=" CD PRO P 240 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 254 " 0.080 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO R 255 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO R 255 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO R 255 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS S 182 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO S 183 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO S 183 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 183 " -0.047 5.00e-02 4.00e+02 ... (remaining 6837 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 561 2.68 - 3.24: 31532 3.24 - 3.79: 49893 3.79 - 4.35: 63329 4.35 - 4.90: 113381 Nonbonded interactions: 258696 Sorted by model distance: nonbonded pdb=" O LEU S 229 " pdb=" OG SER S 241 " model vdw 2.126 2.440 nonbonded pdb=" OD1 ASP N 117 " pdb=" N SER N 118 " model vdw 2.133 2.520 nonbonded pdb=" NH1 ARG B 21 " pdb=" OD1 ASP B 284 " model vdw 2.181 2.520 nonbonded pdb=" O LEU T 229 " pdb=" OG SER T 241 " model vdw 2.203 2.440 nonbonded pdb=" OD1 ASN T 246 " pdb=" N LYS T 247 " model vdw 2.208 2.520 ... (remaining 258691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'L' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 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: 0.030 Extract box with map and model: 13.380 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 95.100 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.003 0.076 38996 Z= 0.175 Angle : 0.575 14.970 53140 Z= 0.304 Chirality : 0.046 0.543 6028 Planarity : 0.007 0.184 6828 Dihedral : 13.058 89.505 14184 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.48 % Allowed : 12.55 % Favored : 86.97 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 4880 helix: 0.65 (0.24), residues: 377 sheet: 0.45 (0.13), residues: 1733 loop : -1.06 (0.11), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 89 HIS 0.005 0.001 HIS O 170 PHE 0.026 0.001 PHE D 436 TYR 0.021 0.001 TYR N 199 ARG 0.005 0.001 ARG O 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 690 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 PHE cc_start: 0.8301 (m-80) cc_final: 0.7712 (m-80) REVERT: D 50 GLU cc_start: 0.7886 (tt0) cc_final: 0.7656 (tt0) REVERT: P 12 THR cc_start: 0.8182 (p) cc_final: 0.7910 (p) REVERT: P 52 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7415 (pp) REVERT: P 199 TYR cc_start: 0.8234 (p90) cc_final: 0.7954 (p90) REVERT: P 266 CYS cc_start: 0.6890 (m) cc_final: 0.6515 (m) REVERT: Q 180 HIS cc_start: 0.8305 (p-80) cc_final: 0.8080 (p90) REVERT: R 254 THR cc_start: 0.8528 (t) cc_final: 0.8310 (p) REVERT: S 155 LYS cc_start: 0.7372 (mtmm) cc_final: 0.7078 (mtmm) REVERT: T 155 LYS cc_start: 0.7699 (mtpp) cc_final: 0.7469 (mtmm) REVERT: T 243 VAL cc_start: 0.8523 (p) cc_final: 0.8200 (t) REVERT: V 34 MET cc_start: 0.6587 (mmm) cc_final: 0.6307 (mmm) outliers start: 20 outliers final: 8 residues processed: 705 average time/residue: 0.5161 time to fit residues: 580.1547 Evaluate side-chains 671 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 662 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain S residue 128 CYS Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 30.0000 chunk 363 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 0.0050 chunk 376 optimal weight: 3.9990 chunk 145 optimal weight: 0.0060 chunk 228 optimal weight: 4.9990 chunk 280 optimal weight: 0.9990 chunk 435 optimal weight: 40.0000 overall best weight: 1.0614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 222 GLN C 152 HIS C 175 ASN C 252 GLN C 389 ASN M 147 HIS M 158 GLN M 218 ASN M 224 GLN M 234 ASN M 245 ASN M 273 ASN N 53 GLN N 130 HIS N 224 GLN N 234 ASN N 273 ASN N 313 HIS N 341 GLN O 53 GLN O 131 HIS O 170 HIS O 193 ASN O 218 ASN O 224 GLN O 299 ASN P 62 HIS P 127 HIS P 218 ASN P 224 GLN P 273 ASN P 299 ASN P 302 GLN P 313 HIS Q 180 HIS Q 190 HIS Q 191 HIS R 139 HIS R 190 HIS S 139 HIS S 220 ASN H 84 ASN L 55 ASN U 33 ASN U 55 ASN W 55 ASN Y 33 ASN Y 55 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 38996 Z= 0.199 Angle : 0.581 12.306 53140 Z= 0.319 Chirality : 0.046 0.414 6028 Planarity : 0.006 0.105 6828 Dihedral : 5.646 57.393 5570 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.52 % Allowed : 12.09 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.11), residues: 4880 helix: 1.71 (0.25), residues: 425 sheet: 0.46 (0.12), residues: 1753 loop : -1.13 (0.11), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 330 HIS 0.006 0.001 HIS Q 139 PHE 0.012 0.001 PHE A 365 TYR 0.012 0.001 TYR A 137 ARG 0.005 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 685 time to evaluate : 4.247 Fit side-chains revert: symmetry clash REVERT: A 76 TYR cc_start: 0.8497 (t80) cc_final: 0.8283 (t80) REVERT: A 138 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6847 (mm-40) REVERT: A 209 GLU cc_start: 0.7113 (mp0) cc_final: 0.6690 (mp0) REVERT: A 345 GLU cc_start: 0.7120 (tt0) cc_final: 0.6909 (tt0) REVERT: B 284 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6950 (t0) REVERT: B 407 MET cc_start: 0.7663 (tpt) cc_final: 0.7189 (tpt) REVERT: B 432 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8407 (mm) REVERT: C 160 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8124 (mtpp) REVERT: C 296 VAL cc_start: 0.8392 (m) cc_final: 0.8007 (t) REVERT: D 130 SER cc_start: 0.8805 (p) cc_final: 0.8422 (m) REVERT: D 347 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7762 (tm-30) REVERT: M 254 LYS cc_start: 0.8687 (ptpt) cc_final: 0.8394 (ptmt) REVERT: M 357 LEU cc_start: 0.8279 (tp) cc_final: 0.7930 (tp) REVERT: N 110 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8479 (m) REVERT: P 12 THR cc_start: 0.8130 (p) cc_final: 0.7828 (p) REVERT: P 52 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7326 (pp) REVERT: P 305 ASN cc_start: 0.8029 (m-40) cc_final: 0.7828 (m-40) REVERT: Q 218 PHE cc_start: 0.7785 (m-80) cc_final: 0.7500 (m-80) REVERT: R 156 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7423 (mtp85) REVERT: T 155 LYS cc_start: 0.7417 (mtpp) cc_final: 0.7072 (mtmm) REVERT: V 98 ARG cc_start: 0.4701 (OUTLIER) cc_final: 0.4355 (ptt180) outliers start: 105 outliers final: 62 residues processed: 743 average time/residue: 0.5119 time to fit residues: 613.7374 Evaluate side-chains 707 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 640 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 384 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 313 HIS Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 193 ASN Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 223 ASP Chi-restraints excluded: chain P residue 313 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 390 VAL Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 146 ASN Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 247 LYS Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain T residue 251 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 98 ARG Chi-restraints excluded: chain V residue 105 ASP Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 362 optimal weight: 0.6980 chunk 296 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 436 optimal weight: 3.9990 chunk 471 optimal weight: 0.2980 chunk 388 optimal weight: 0.0050 chunk 433 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 350 optimal weight: 10.0000 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN C 138 GLN C 252 GLN M 218 ASN M 313 HIS N 183 GLN N 313 HIS P 130 HIS P 218 ASN Q 195 GLN R 139 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 38996 Z= 0.137 Angle : 0.516 10.185 53140 Z= 0.278 Chirality : 0.044 0.343 6028 Planarity : 0.005 0.075 6828 Dihedral : 5.236 53.688 5563 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.55 % Allowed : 13.27 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.12), residues: 4880 helix: 1.78 (0.26), residues: 427 sheet: 0.48 (0.13), residues: 1716 loop : -1.05 (0.11), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 330 HIS 0.015 0.001 HIS N 313 PHE 0.010 0.001 PHE O 115 TYR 0.012 0.001 TYR N 199 ARG 0.006 0.000 ARG N 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 659 time to evaluate : 3.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8081 (mt) cc_final: 0.7703 (mp) REVERT: A 209 GLU cc_start: 0.7132 (mp0) cc_final: 0.6706 (mp0) REVERT: B 7 ILE cc_start: 0.8199 (mt) cc_final: 0.7981 (pt) REVERT: B 160 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7275 (mttt) REVERT: B 284 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7015 (t70) REVERT: B 432 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8293 (mm) REVERT: C 160 LYS cc_start: 0.8299 (mtmt) cc_final: 0.8053 (mtpp) REVERT: C 417 VAL cc_start: 0.8107 (t) cc_final: 0.7892 (t) REVERT: D 130 SER cc_start: 0.8790 (p) cc_final: 0.8402 (m) REVERT: D 347 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7794 (tm-30) REVERT: M 212 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8373 (m) REVERT: M 251 ARG cc_start: 0.8121 (mtp180) cc_final: 0.7740 (ttp80) REVERT: M 254 LYS cc_start: 0.8618 (ptpt) cc_final: 0.8324 (ptmt) REVERT: M 291 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.6667 (p90) REVERT: M 357 LEU cc_start: 0.8383 (tp) cc_final: 0.8051 (tp) REVERT: N 200 LYS cc_start: 0.7636 (tttt) cc_final: 0.7293 (tttm) REVERT: O 394 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8222 (ttp80) REVERT: O 398 THR cc_start: 0.7638 (m) cc_final: 0.7162 (m) REVERT: P 12 THR cc_start: 0.7944 (p) cc_final: 0.7715 (p) REVERT: P 52 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7261 (pp) REVERT: P 117 ASP cc_start: 0.7262 (t0) cc_final: 0.7026 (t70) REVERT: P 291 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.6872 (p-80) REVERT: Q 180 HIS cc_start: 0.7910 (p90) cc_final: 0.7706 (p90) REVERT: Q 218 PHE cc_start: 0.7777 (m-80) cc_final: 0.7516 (m-80) REVERT: T 130 VAL cc_start: 0.7807 (t) cc_final: 0.7544 (p) outliers start: 106 outliers final: 59 residues processed: 717 average time/residue: 0.4887 time to fit residues: 566.5415 Evaluate side-chains 693 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 627 time to evaluate : 4.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 381 MET Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 223 ASP Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain T residue 251 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 9.9990 chunk 328 optimal weight: 0.6980 chunk 226 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 438 optimal weight: 7.9990 chunk 463 optimal weight: 50.0000 chunk 228 optimal weight: 4.9990 chunk 415 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN C 252 GLN M 218 ASN M 313 HIS P 62 HIS P 218 ASN Q 195 GLN R 139 HIS R 170 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 38996 Z= 0.202 Angle : 0.550 10.237 53140 Z= 0.296 Chirality : 0.045 0.326 6028 Planarity : 0.005 0.066 6828 Dihedral : 5.287 58.147 5561 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.76 % Allowed : 14.09 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 4880 helix: 1.89 (0.26), residues: 425 sheet: 0.37 (0.13), residues: 1720 loop : -1.10 (0.11), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 330 HIS 0.021 0.001 HIS R 139 PHE 0.015 0.001 PHE A 365 TYR 0.013 0.001 TYR A 46 ARG 0.009 0.000 ARG P 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 665 time to evaluate : 3.716 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: A 29 LEU cc_start: 0.8128 (mt) cc_final: 0.7770 (mp) REVERT: A 138 GLN cc_start: 0.7107 (mm-40) cc_final: 0.6895 (mm-40) REVERT: A 196 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7578 (mmm-85) REVERT: A 209 GLU cc_start: 0.7181 (mp0) cc_final: 0.6747 (mp0) REVERT: B 284 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7197 (t0) REVERT: B 300 SER cc_start: 0.7761 (p) cc_final: 0.7503 (p) REVERT: B 432 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8305 (mm) REVERT: C 160 LYS cc_start: 0.8301 (mtmt) cc_final: 0.8050 (mtpp) REVERT: C 417 VAL cc_start: 0.8208 (t) cc_final: 0.8002 (t) REVERT: D 130 SER cc_start: 0.8799 (p) cc_final: 0.8402 (m) REVERT: M 212 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8398 (m) REVERT: M 251 ARG cc_start: 0.8200 (mtp180) cc_final: 0.7759 (ttp80) REVERT: M 291 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6829 (p90) REVERT: M 408 VAL cc_start: 0.8607 (t) cc_final: 0.8332 (p) REVERT: N 13 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8269 (ptt180) REVERT: N 200 LYS cc_start: 0.7575 (tttt) cc_final: 0.7208 (tttm) REVERT: N 212 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7223 (t) REVERT: N 394 ARG cc_start: 0.7749 (mtp85) cc_final: 0.7465 (mtm-85) REVERT: O 373 VAL cc_start: 0.8231 (t) cc_final: 0.7930 (m) REVERT: O 394 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8172 (ttp80) REVERT: O 398 THR cc_start: 0.7578 (m) cc_final: 0.7139 (m) REVERT: P 12 THR cc_start: 0.8072 (p) cc_final: 0.7797 (p) REVERT: P 52 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7323 (pp) REVERT: P 117 ASP cc_start: 0.7304 (t0) cc_final: 0.7054 (t70) REVERT: P 263 ASN cc_start: 0.7624 (m-40) cc_final: 0.7410 (m110) REVERT: P 291 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7197 (p-80) REVERT: Q 218 PHE cc_start: 0.7802 (m-80) cc_final: 0.7532 (m-80) REVERT: V 34 MET cc_start: 0.6995 (mmm) cc_final: 0.6081 (tmm) outliers start: 115 outliers final: 90 residues processed: 729 average time/residue: 0.5340 time to fit residues: 633.4496 Evaluate side-chains 740 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 642 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 313 HIS Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 381 MET Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 223 ASP Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 390 VAL Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain P residue 408 VAL Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 252 LYS Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 345 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 395 optimal weight: 0.9980 chunk 320 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 416 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN C 252 GLN M 131 HIS M 218 ASN N 193 ASN N 245 ASN N 313 HIS O 218 ASN P 62 HIS P 183 GLN P 313 HIS Q 195 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 38996 Z= 0.234 Angle : 0.566 10.542 53140 Z= 0.306 Chirality : 0.046 0.321 6028 Planarity : 0.005 0.050 6828 Dihedral : 5.377 59.422 5561 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.37 % Allowed : 14.64 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 4880 helix: 2.00 (0.26), residues: 416 sheet: 0.32 (0.13), residues: 1699 loop : -1.24 (0.11), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Y 37 HIS 0.031 0.001 HIS M 313 PHE 0.015 0.001 PHE A 365 TYR 0.015 0.001 TYR A 46 ARG 0.008 0.000 ARG S 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 644 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8136 (mt) cc_final: 0.7779 (mp) REVERT: A 138 GLN cc_start: 0.7184 (mm-40) cc_final: 0.6968 (mt0) REVERT: A 196 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.7548 (mmm-85) REVERT: A 209 GLU cc_start: 0.7156 (mp0) cc_final: 0.6727 (mp0) REVERT: B 432 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8299 (mm) REVERT: C 13 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.8053 (m) REVERT: D 109 GLU cc_start: 0.7783 (tt0) cc_final: 0.7542 (tt0) REVERT: D 130 SER cc_start: 0.8811 (p) cc_final: 0.8425 (m) REVERT: D 430 VAL cc_start: 0.8075 (t) cc_final: 0.7746 (p) REVERT: M 110 THR cc_start: 0.8418 (p) cc_final: 0.8152 (m) REVERT: M 212 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8434 (m) REVERT: M 251 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7914 (ttp80) REVERT: N 13 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8422 (ptt180) REVERT: N 293 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8330 (m) REVERT: O 373 VAL cc_start: 0.8235 (t) cc_final: 0.7936 (m) REVERT: O 394 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8395 (ttp80) REVERT: O 398 THR cc_start: 0.7563 (m) cc_final: 0.7130 (m) REVERT: P 52 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7365 (pp) REVERT: P 117 ASP cc_start: 0.7288 (t0) cc_final: 0.7053 (t70) REVERT: P 291 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7279 (p-80) REVERT: R 124 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6347 (pmm) REVERT: V 34 MET cc_start: 0.6914 (mmm) cc_final: 0.5996 (tmm) outliers start: 140 outliers final: 107 residues processed: 724 average time/residue: 0.4844 time to fit residues: 566.9003 Evaluate side-chains 746 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 631 time to evaluate : 3.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 388 MET Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 313 HIS Chi-restraints excluded: chain N residue 381 MET Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 355 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 223 ASP Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 313 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 390 VAL Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain P residue 408 VAL Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 241 SER Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 252 LYS Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 1.9990 chunk 417 optimal weight: 8.9990 chunk 91 optimal weight: 0.0670 chunk 272 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 464 optimal weight: 30.0000 chunk 385 optimal weight: 1.9990 chunk 215 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN C 252 GLN M 218 ASN M 313 HIS N 313 HIS O 218 ASN P 62 HIS Q 195 GLN S 139 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38996 Z= 0.172 Angle : 0.535 9.770 53140 Z= 0.287 Chirality : 0.045 0.619 6028 Planarity : 0.005 0.048 6828 Dihedral : 5.303 58.550 5561 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.32 % Allowed : 15.12 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 4880 helix: 1.97 (0.26), residues: 421 sheet: 0.32 (0.13), residues: 1648 loop : -1.22 (0.10), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 37 HIS 0.024 0.001 HIS N 313 PHE 0.012 0.001 PHE A 365 TYR 0.017 0.001 TYR S 160 ARG 0.006 0.000 ARG P 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 638 time to evaluate : 3.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8130 (mt) cc_final: 0.7748 (mp) REVERT: A 123 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7794 (ttm170) REVERT: A 138 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6932 (mt0) REVERT: A 196 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7525 (mmm-85) REVERT: A 209 GLU cc_start: 0.7206 (mp0) cc_final: 0.6788 (mp0) REVERT: B 432 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8256 (mm) REVERT: C 13 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.8020 (m) REVERT: C 133 LEU cc_start: 0.8446 (mt) cc_final: 0.8234 (mt) REVERT: D 109 GLU cc_start: 0.7750 (tt0) cc_final: 0.7504 (tt0) REVERT: D 130 SER cc_start: 0.8808 (p) cc_final: 0.8423 (m) REVERT: D 430 VAL cc_start: 0.8045 (t) cc_final: 0.7714 (p) REVERT: M 110 THR cc_start: 0.8395 (p) cc_final: 0.8127 (m) REVERT: M 212 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8421 (m) REVERT: M 251 ARG cc_start: 0.8229 (mtp180) cc_final: 0.7964 (ttp80) REVERT: M 291 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6620 (p-80) REVERT: N 13 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8394 (ptt180) REVERT: N 87 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.6840 (p) REVERT: N 212 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.7178 (t) REVERT: N 286 LEU cc_start: 0.8536 (tt) cc_final: 0.8276 (tp) REVERT: N 293 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8282 (m) REVERT: N 375 SER cc_start: 0.8325 (t) cc_final: 0.7977 (p) REVERT: O 373 VAL cc_start: 0.8149 (t) cc_final: 0.7861 (m) REVERT: O 394 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8366 (ttp80) REVERT: O 398 THR cc_start: 0.7251 (m) cc_final: 0.6861 (m) REVERT: P 52 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7303 (pp) REVERT: P 117 ASP cc_start: 0.7225 (t0) cc_final: 0.7001 (t70) REVERT: P 291 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7308 (p-80) REVERT: R 124 MET cc_start: 0.6662 (pmm) cc_final: 0.6385 (pmm) REVERT: V 34 MET cc_start: 0.6950 (mmm) cc_final: 0.5930 (tmm) outliers start: 138 outliers final: 100 residues processed: 721 average time/residue: 0.4785 time to fit residues: 560.7122 Evaluate side-chains 730 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 620 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 381 MET Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 355 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 223 ASP Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 390 VAL Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain P residue 408 VAL Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 252 LYS Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 40.0000 chunk 52 optimal weight: 0.0570 chunk 264 optimal weight: 3.9990 chunk 339 optimal weight: 0.9990 chunk 262 optimal weight: 0.6980 chunk 390 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 462 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN C 252 GLN M 218 ASN M 313 HIS N 158 GLN N 313 HIS O 193 ASN O 218 ASN P 62 HIS Q 195 GLN R 191 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 38996 Z= 0.248 Angle : 0.578 9.641 53140 Z= 0.314 Chirality : 0.046 0.521 6028 Planarity : 0.006 0.053 6828 Dihedral : 5.422 54.229 5561 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.27 % Allowed : 15.22 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 4880 helix: 1.88 (0.26), residues: 422 sheet: 0.27 (0.13), residues: 1573 loop : -1.35 (0.10), residues: 2885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 189 HIS 0.008 0.001 HIS N 99 PHE 0.017 0.001 PHE A 365 TYR 0.016 0.002 TYR S 160 ARG 0.006 0.000 ARG P 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 645 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8590 (t) cc_final: 0.8284 (m) REVERT: A 29 LEU cc_start: 0.8150 (mt) cc_final: 0.7810 (mp) REVERT: A 123 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7804 (ttm170) REVERT: A 138 GLN cc_start: 0.7242 (mm-40) cc_final: 0.7024 (mt0) REVERT: A 196 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7519 (mmm-85) REVERT: A 209 GLU cc_start: 0.7180 (mp0) cc_final: 0.6745 (mp0) REVERT: A 427 ILE cc_start: 0.8924 (mm) cc_final: 0.8638 (tt) REVERT: C 13 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8069 (m) REVERT: C 133 LEU cc_start: 0.8472 (mt) cc_final: 0.8251 (mt) REVERT: D 130 SER cc_start: 0.8812 (p) cc_final: 0.8447 (m) REVERT: D 430 VAL cc_start: 0.8061 (t) cc_final: 0.7763 (p) REVERT: M 212 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8468 (m) REVERT: M 291 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.6797 (p-80) REVERT: N 87 THR cc_start: 0.7324 (OUTLIER) cc_final: 0.6771 (p) REVERT: N 147 HIS cc_start: 0.7877 (t-90) cc_final: 0.7661 (t70) REVERT: N 212 THR cc_start: 0.7402 (OUTLIER) cc_final: 0.7141 (t) REVERT: N 286 LEU cc_start: 0.8566 (tt) cc_final: 0.8314 (tp) REVERT: N 293 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8351 (m) REVERT: O 373 VAL cc_start: 0.8227 (t) cc_final: 0.7939 (m) REVERT: O 394 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8367 (ttp80) REVERT: O 398 THR cc_start: 0.7346 (m) cc_final: 0.6982 (m) REVERT: P 52 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7382 (pp) REVERT: P 291 HIS cc_start: 0.8062 (OUTLIER) cc_final: 0.7414 (p-80) REVERT: R 124 MET cc_start: 0.6601 (pmm) cc_final: 0.6393 (pmm) REVERT: V 34 MET cc_start: 0.7020 (mmm) cc_final: 0.5955 (tmm) outliers start: 136 outliers final: 108 residues processed: 730 average time/residue: 0.4823 time to fit residues: 571.8644 Evaluate side-chains 759 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 643 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 381 MET Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 355 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 223 ASP Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 390 VAL Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain P residue 408 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 241 SER Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 5.9990 chunk 184 optimal weight: 0.1980 chunk 276 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 294 optimal weight: 0.8980 chunk 315 optimal weight: 3.9990 chunk 228 optimal weight: 0.0270 chunk 43 optimal weight: 5.9990 chunk 363 optimal weight: 7.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 GLN M 53 GLN M 158 GLN M 218 ASN M 313 HIS N 158 GLN N 245 ASN N 313 HIS O 193 ASN O 218 ASN P 62 HIS P 313 HIS Q 195 GLN S 139 HIS L 33 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 38996 Z= 0.145 Angle : 0.516 11.597 53140 Z= 0.273 Chirality : 0.044 0.464 6028 Planarity : 0.005 0.048 6828 Dihedral : 5.182 57.002 5561 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.67 % Allowed : 16.27 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.12), residues: 4880 helix: 2.08 (0.27), residues: 421 sheet: 0.33 (0.13), residues: 1593 loop : -1.23 (0.11), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 89 HIS 0.008 0.001 HIS N 313 PHE 0.009 0.001 PHE A 365 TYR 0.015 0.001 TYR S 160 ARG 0.007 0.000 ARG S 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 633 time to evaluate : 4.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8492 (t) cc_final: 0.8144 (m) REVERT: A 29 LEU cc_start: 0.8132 (mt) cc_final: 0.7755 (mp) REVERT: A 123 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7763 (ttm170) REVERT: A 138 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6890 (mt0) REVERT: A 209 GLU cc_start: 0.7189 (mp0) cc_final: 0.6777 (mp0) REVERT: A 402 ILE cc_start: 0.8549 (pt) cc_final: 0.8272 (mt) REVERT: B 257 PHE cc_start: 0.8142 (m-80) cc_final: 0.7696 (m-80) REVERT: B 432 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8202 (mm) REVERT: C 13 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7964 (m) REVERT: C 133 LEU cc_start: 0.8432 (mt) cc_final: 0.8211 (mt) REVERT: C 417 VAL cc_start: 0.8145 (t) cc_final: 0.7900 (t) REVERT: D 109 GLU cc_start: 0.7698 (tt0) cc_final: 0.7458 (tt0) REVERT: D 130 SER cc_start: 0.8801 (p) cc_final: 0.8431 (m) REVERT: D 430 VAL cc_start: 0.8041 (t) cc_final: 0.7689 (p) REVERT: M 212 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8435 (m) REVERT: M 251 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7897 (ttp80) REVERT: M 386 VAL cc_start: 0.8444 (t) cc_final: 0.8232 (p) REVERT: N 87 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6610 (p) REVERT: N 212 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.7107 (t) REVERT: N 293 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8272 (m) REVERT: O 373 VAL cc_start: 0.7979 (t) cc_final: 0.7706 (m) REVERT: P 52 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7243 (pp) REVERT: P 70 MET cc_start: 0.8154 (tpp) cc_final: 0.7361 (ttm) REVERT: P 254 LYS cc_start: 0.8543 (ptpt) cc_final: 0.8137 (mtpt) REVERT: S 132 ASP cc_start: 0.7961 (p0) cc_final: 0.7578 (p0) REVERT: V 34 MET cc_start: 0.7042 (mmm) cc_final: 0.5948 (tmm) outliers start: 111 outliers final: 89 residues processed: 701 average time/residue: 0.4847 time to fit residues: 553.5795 Evaluate side-chains 718 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 622 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 261 LEU Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 381 MET Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 193 ASN Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 355 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 313 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain P residue 408 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain X residue 60 TYR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 9.9990 chunk 443 optimal weight: 8.9990 chunk 404 optimal weight: 20.0000 chunk 431 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 338 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 389 optimal weight: 9.9990 chunk 407 optimal weight: 0.9990 chunk 429 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS C 252 GLN C 375 HIS ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 218 ASN M 313 HIS N 193 ASN N 313 HIS ** O 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 218 ASN P 62 HIS Q 195 GLN T 190 HIS L 33 ASN U 33 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 38996 Z= 0.419 Angle : 0.704 11.734 53140 Z= 0.384 Chirality : 0.051 0.516 6028 Planarity : 0.007 0.064 6828 Dihedral : 5.740 57.516 5561 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.08 % Allowed : 16.13 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.00 (0.11), residues: 4880 helix: 1.60 (0.26), residues: 419 sheet: 0.21 (0.14), residues: 1497 loop : -1.55 (0.10), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 189 HIS 0.012 0.002 HIS N 99 PHE 0.022 0.002 PHE A 365 TYR 0.026 0.002 TYR D 51 ARG 0.006 0.001 ARG N 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 650 time to evaluate : 4.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 13 VAL cc_start: 0.8580 (t) cc_final: 0.8310 (m) REVERT: A 123 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7900 (ttm-80) REVERT: A 209 GLU cc_start: 0.7244 (mp0) cc_final: 0.6889 (mp0) REVERT: A 402 ILE cc_start: 0.8641 (pt) cc_final: 0.8407 (mt) REVERT: A 427 ILE cc_start: 0.8922 (mm) cc_final: 0.8664 (tt) REVERT: C 366 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7782 (mtp85) REVERT: D 130 SER cc_start: 0.8818 (p) cc_final: 0.8477 (m) REVERT: D 311 ASP cc_start: 0.7566 (t0) cc_final: 0.7337 (t0) REVERT: D 430 VAL cc_start: 0.8051 (t) cc_final: 0.7797 (p) REVERT: M 87 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7186 (p) REVERT: M 277 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8118 (p) REVERT: N 87 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.6804 (p) REVERT: N 181 MET cc_start: 0.7610 (mtp) cc_final: 0.7404 (mtp) REVERT: N 261 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (mt) REVERT: N 366 MET cc_start: 0.7407 (mmm) cc_final: 0.7011 (mmt) REVERT: N 397 ILE cc_start: 0.7746 (tp) cc_final: 0.7485 (tt) REVERT: O 373 VAL cc_start: 0.8533 (t) cc_final: 0.8211 (m) REVERT: P 52 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7497 (pp) REVERT: P 291 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7613 (p-80) REVERT: P 394 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7372 (ttm-80) REVERT: R 122 LYS cc_start: 0.7416 (mttt) cc_final: 0.7187 (mtmm) REVERT: S 132 ASP cc_start: 0.8051 (p0) cc_final: 0.7658 (p0) REVERT: T 243 VAL cc_start: 0.8476 (p) cc_final: 0.8202 (t) REVERT: H 53 THR cc_start: 0.8368 (p) cc_final: 0.8041 (p) REVERT: V 48 MET cc_start: 0.4417 (mtm) cc_final: 0.2880 (mtm) outliers start: 128 outliers final: 98 residues processed: 733 average time/residue: 0.5242 time to fit residues: 619.8072 Evaluate side-chains 753 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 649 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 261 LEU Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 381 MET Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 355 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain P residue 408 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 241 SER Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 1.9990 chunk 455 optimal weight: 7.9990 chunk 278 optimal weight: 0.0270 chunk 216 optimal weight: 0.7980 chunk 316 optimal weight: 6.9990 chunk 478 optimal weight: 30.0000 chunk 440 optimal weight: 20.0000 chunk 380 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 GLN M 53 GLN M 218 ASN N 158 GLN N 313 HIS O 193 ASN O 218 ASN O 299 ASN P 62 HIS P 313 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38996 Z= 0.255 Angle : 0.595 9.550 53140 Z= 0.321 Chirality : 0.047 0.476 6028 Planarity : 0.006 0.059 6828 Dihedral : 5.533 59.298 5561 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.69 % Allowed : 16.61 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.11), residues: 4880 helix: 1.68 (0.26), residues: 422 sheet: 0.06 (0.13), residues: 1600 loop : -1.54 (0.10), residues: 2858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 235 HIS 0.008 0.001 HIS N 99 PHE 0.017 0.001 PHE A 365 TYR 0.018 0.002 TYR S 160 ARG 0.005 0.000 ARG S 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 618 time to evaluate : 4.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8547 (t) cc_final: 0.8259 (m) REVERT: A 29 LEU cc_start: 0.8166 (mt) cc_final: 0.7814 (mp) REVERT: A 123 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7898 (ttm-80) REVERT: A 209 GLU cc_start: 0.7240 (mp0) cc_final: 0.6859 (mp0) REVERT: A 402 ILE cc_start: 0.8628 (pt) cc_final: 0.8381 (mt) REVERT: A 427 ILE cc_start: 0.8903 (mm) cc_final: 0.8643 (tt) REVERT: C 133 LEU cc_start: 0.8464 (mt) cc_final: 0.8247 (mt) REVERT: D 130 SER cc_start: 0.8777 (p) cc_final: 0.8476 (m) REVERT: D 284 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7466 (t0) REVERT: D 430 VAL cc_start: 0.8059 (t) cc_final: 0.7750 (p) REVERT: M 87 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.6830 (p) REVERT: M 212 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8499 (m) REVERT: N 87 THR cc_start: 0.7151 (OUTLIER) cc_final: 0.6571 (p) REVERT: N 212 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7184 (t) REVERT: N 261 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7979 (mt) REVERT: N 293 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8344 (m) REVERT: N 366 MET cc_start: 0.7310 (mmm) cc_final: 0.6918 (mmt) REVERT: O 373 VAL cc_start: 0.8351 (t) cc_final: 0.8033 (m) REVERT: P 52 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7379 (pp) REVERT: P 70 MET cc_start: 0.8328 (tpp) cc_final: 0.7489 (ttm) REVERT: P 254 LYS cc_start: 0.8648 (ptpt) cc_final: 0.8253 (mtpt) REVERT: P 291 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7348 (p-80) REVERT: P 305 ASN cc_start: 0.8213 (m-40) cc_final: 0.7972 (m-40) REVERT: P 394 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.7292 (ttm-80) REVERT: Q 205 THR cc_start: 0.7533 (t) cc_final: 0.7136 (m) REVERT: R 122 LYS cc_start: 0.7360 (mttt) cc_final: 0.7120 (mtmm) REVERT: S 132 ASP cc_start: 0.8002 (p0) cc_final: 0.7617 (p0) REVERT: T 155 LYS cc_start: 0.7851 (mtpp) cc_final: 0.7485 (mtmt) REVERT: H 53 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8033 (p) REVERT: V 48 MET cc_start: 0.4701 (mtm) cc_final: 0.3299 (mtm) outliers start: 112 outliers final: 95 residues processed: 689 average time/residue: 0.5090 time to fit residues: 567.9752 Evaluate side-chains 719 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 614 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 220 CYS Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 261 LEU Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 381 MET Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 193 ASN Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 355 ILE Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 313 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain P residue 408 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 241 SER Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 1.9990 chunk 405 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 351 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 105 optimal weight: 0.0870 chunk 381 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 391 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 GLN M 53 GLN M 218 ASN N 158 GLN N 313 HIS O 193 ASN O 218 ASN O 299 ASN P 313 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110107 restraints weight = 59863.257| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.39 r_work: 0.3166 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 38996 Z= 0.185 Angle : 0.676 59.198 53140 Z= 0.379 Chirality : 0.046 0.467 6028 Planarity : 0.006 0.113 6828 Dihedral : 5.518 59.144 5561 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.74 % Allowed : 16.75 % Favored : 80.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.78 % 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: -1.00 (0.11), residues: 4880 helix: 1.75 (0.26), residues: 422 sheet: 0.07 (0.13), residues: 1610 loop : -1.56 (0.10), residues: 2848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 235 HIS 0.114 0.002 HIS P 313 PHE 0.014 0.001 PHE A 365 TYR 0.017 0.001 TYR S 160 ARG 0.004 0.000 ARG P 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11157.21 seconds wall clock time: 200 minutes 4.13 seconds (12004.13 seconds total)