Starting phenix.real_space_refine on Sat Mar 23 16:59:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dww_27763/03_2024/8dww_27763.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dww_27763/03_2024/8dww_27763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dww_27763/03_2024/8dww_27763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dww_27763/03_2024/8dww_27763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dww_27763/03_2024/8dww_27763.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dww_27763/03_2024/8dww_27763.pdb" } resolution = 3.13 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= 0.050 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 23856 2.51 5 N 6520 2.21 5 O 7264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 2": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 281": "OD1" <-> "OD2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 24": "OE1" <-> "OE2" Residue "N GLU 109": "OE1" <-> "OE2" Residue "N GLU 150": "OE1" <-> "OE2" Residue "N ASP 177": "OD1" <-> "OD2" Residue "N TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 303": "OE1" <-> "OE2" Residue "N GLU 324": "OE1" <-> "OE2" Residue "R ASP 132": "OD1" <-> "OD2" Residue "R TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ASP 281": "OD1" <-> "OD2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "V TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 60": "OD1" <-> "OD2" Residue "M ASP 63": "OD1" <-> "OD2" Residue "M ASP 77": "OD1" <-> "OD2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ASP 174": "OD1" <-> "OD2" Residue "M ASP 177": "OD1" <-> "OD2" Residue "M ASP 214": "OD1" <-> "OD2" Residue "M GLU 247": "OE1" <-> "OE2" Residue "M GLU 303": "OE1" <-> "OE2" Residue "Q ASP 161": "OD1" <-> "OD2" Residue "Q GLU 234": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ASP 343": "OD1" <-> "OD2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 21": "OD1" <-> "OD2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 132": "OE1" <-> "OE2" Residue "O GLU 168": "OE1" <-> "OE2" Residue "O ASP 177": "OD1" <-> "OD2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 214": "OD1" <-> "OD2" Residue "O ASP 290": "OD1" <-> "OD2" Residue "O TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 361": "OE1" <-> "OE2" Residue "O TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 112": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D ASP 284": "OD1" <-> "OD2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ASP 385": "OD1" <-> "OD2" Residue "D ASP 401": "OD1" <-> "OD2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 21": "OD1" <-> "OD2" Residue "P ASP 77": "OD1" <-> "OD2" Residue "P ASP 177": "OD1" <-> "OD2" Residue "P TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 308": "OE1" <-> "OE2" Residue "P GLU 309": "OE1" <-> "OE2" Residue "P GLU 316": "OE1" <-> "OE2" Residue "P TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37900 Number of models: 1 Model: "" Number of chains: 28 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: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} 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: "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: "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: "V" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "U" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} 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: "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: "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: "X" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "W" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} 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: "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: "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: "Z" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "Y" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: 37900 At special positions: 0 Unit cell: (185.6, 212.28, 241.28, 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 7264 8.00 N 6520 7.00 C 23856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=68, symmetry=0 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=2.04 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 H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 125 " distance=2.03 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 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=2.04 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 V 22 " - pdb=" SG CYS V 96 " distance=2.04 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 266 " distance=2.03 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 C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.04 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 X 22 " - pdb=" SG CYS X 96 " distance=2.04 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 125 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 28 " distance=2.02 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 105 " distance=2.04 Simple disulfide: pdb=" SG CYS O 153 " - pdb=" SG CYS O 266 " distance=2.03 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 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=2.04 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 Z 22 " - pdb=" SG CYS Z 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " 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 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: 13.22 Conformation dependent library (CDL) restraints added in 7.4 seconds 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9096 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 105 sheets defined 12.8% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.971A pdb=" N TYR B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 246 " --> pdb=" O TYR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.743A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 403 through 439 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.766A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.128A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 10 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 361 Processing helix chain 'N' and resid 363 through 403 removed outlier: 3.551A pdb=" N ALA N 385 " --> pdb=" O MET N 381 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.530A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) removed outlier: 3.523A 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 'R' and resid 148 through 152 Processing helix chain 'R' and resid 168 through 175 removed outlier: 5.036A pdb=" N SER R 173 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.548A pdb=" N LYS A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 4.003A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.583A pdb=" N THR A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 439 removed outlier: 3.502A pdb=" N ILE A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 32 Processing helix chain 'V' and resid 62 through 65 removed outlier: 3.741A pdb=" N LYS V 65 " --> pdb=" O ASP V 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 62 through 65' Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.982A pdb=" N PHE U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 10 Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing helix chain 'M' and resid 351 through 361 removed outlier: 3.599A pdb=" N LEU M 357 " --> pdb=" O HIS M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 398 removed outlier: 3.505A pdb=" N VAL M 368 " --> pdb=" O PRO M 364 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 402 Processing helix chain 'M' 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: 5.157A pdb=" N SER Q 173 " --> pdb=" O HIS Q 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.685A pdb=" N LYS C 115 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 4.185A pdb=" N TYR C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.633A pdb=" N THR C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 259 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 403 through 439 Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 62 through 65 removed outlier: 3.821A pdb=" N LYS X 65 " --> pdb=" O ASP X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 62 through 65' Processing helix chain 'W' and resid 79 through 83 removed outlier: 3.833A pdb=" N PHE W 83 " --> pdb=" O PRO W 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 10 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 361 removed outlier: 3.552A pdb=" N LEU O 357 " --> pdb=" O HIS O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 403 Proline residue: O 399 - end of helix removed outlier: 3.609A pdb=" N THR O 403 " --> pdb=" O PRO O 399 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 415 Processing helix chain 'S' and resid 148 through 152 removed outlier: 3.550A pdb=" N LYS S 151 " --> pdb=" O ASP S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 175 removed outlier: 5.184A pdb=" N SER S 173 " --> pdb=" O HIS S 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.559A pdb=" N LYS D 115 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.993A pdb=" N TYR D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 246 " --> pdb=" O TYR D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.770A pdb=" N THR D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 403 through 439 removed outlier: 3.502A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 32 Processing helix chain 'Y' and resid 79 through 83 removed outlier: 3.953A pdb=" N PHE Y 83 " --> pdb=" O PRO Y 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 10 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: 3.540A pdb=" N LEU P 357 " --> pdb=" O HIS P 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 403 removed outlier: 3.594A pdb=" N VAL P 368 " --> pdb=" O PRO P 364 " (cutoff:3.500A) Proline residue: P 399 - end of helix removed outlier: 3.698A pdb=" N LEU P 402 " --> pdb=" O THR P 398 " (cutoff:3.500A) removed outlier: 3.611A 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 'T' and resid 148 through 152 Processing helix chain 'T' and resid 168 through 175 removed outlier: 4.993A pdb=" N SER T 173 " --> pdb=" O HIS T 170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.729A pdb=" N LYS B 160 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 15 through 19 removed outlier: 4.073A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS B 132 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR B 126 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 42 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA B 124 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 44 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B 122 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 46 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER B 120 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 120 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 140 through 147 removed outlier: 4.910A pdb=" N SER B 120 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 46 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B 122 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 44 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA B 124 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 42 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR B 126 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS B 132 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.506A pdb=" N ALA B 106 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA8, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 296 through 306 removed outlier: 4.518A pdb=" N ASP B 298 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB2, first strand: chain 'B' and resid 387 through 388 removed outlier: 3.541A pdb=" N TYR N 297 " --> pdb=" O HIS N 307 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.064A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.064A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.152A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 17 through 19 Processing sheet with id=AB9, first strand: chain 'N' and resid 74 through 79 removed outlier: 6.004A pdb=" N LYS N 66 " --> pdb=" O GLY N 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN N 53 " --> pdb=" O ARG N 68 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET N 70 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N SER N 51 " --> pdb=" O MET N 70 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N HIS N 99 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N LEU N 52 " --> pdb=" O MET N 97 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N MET N 97 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N ILE N 54 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLY N 95 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 17.002A pdb=" N ILE N 56 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 19.906A pdb=" N ILE N 93 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 84 through 86 removed outlier: 4.336A pdb=" N GLU N 109 " --> pdb=" O PHE N 129 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 148 through 156 Processing sheet with id=AC3, first strand: chain 'N' and resid 236 through 237 removed outlier: 4.085A pdb=" N GLY N 253 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 175 through 176 removed outlier: 3.694A pdb=" N GLY N 209 " --> pdb=" O TYR N 199 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 181 through 184 Processing sheet with id=AC6, first strand: chain 'N' and resid 275 through 279 removed outlier: 3.883A pdb=" N LYS N 315 " --> pdb=" O LEU N 287 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 143 through 144 removed outlier: 3.541A pdb=" N GLY R 125 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS R 119 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL R 123 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TYR R 126 " --> pdb=" O PRO R 137 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 249 through 253 removed outlier: 5.315A pdb=" N PHE R 201 " --> pdb=" O LEU R 240 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N ALA R 193 " --> pdb=" O PRO R 204 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY R 185 " --> pdb=" O TYR R 196 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE R 217 " --> pdb=" O VAL R 225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 249 through 253 removed outlier: 4.369A pdb=" N ALA R 239 " --> pdb=" O ALA R 232 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY R 230 " --> pdb=" O SER R 241 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL R 243 " --> pdb=" O VAL R 228 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL R 228 " --> pdb=" O VAL R 243 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N TRP R 245 " --> pdb=" O ALA R 226 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA R 226 " --> pdb=" O TRP R 245 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AD2, first strand: chain 'A' and resid 15 through 19 removed outlier: 3.805A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS A 132 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 42 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 124 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR A 46 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 120 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 140 through 147 removed outlier: 4.999A pdb=" N SER A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR A 46 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 124 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 42 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS A 132 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.539A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.539A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 106 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AD7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AD8, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AD9, first strand: chain 'A' and resid 296 through 306 removed outlier: 4.491A pdb=" N ASP A 298 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 300 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 315 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AE2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AE3, first strand: chain 'V' and resid 3 through 7 removed outlier: 3.511A pdb=" N SER V 21 " --> pdb=" O SER V 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 10 through 12 removed outlier: 6.138A pdb=" N GLY V 10 " --> pdb=" O THR V 117 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR V 114 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N MET V 34 " --> pdb=" O TYR V 50 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR V 50 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP V 36 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR V 50 " --> pdb=" O HIS V 59 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 10 through 12 removed outlier: 6.138A pdb=" N GLY V 10 " --> pdb=" O THR V 117 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR V 114 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR V 109 " --> pdb=" O ARG V 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 4 through 7 removed outlier: 3.749A pdb=" N VAL U 19 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.037A pdb=" N LEU U 11 " --> pdb=" O GLU U 105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 17 through 19 Processing sheet with id=AE9, first strand: chain 'M' and resid 74 through 79 removed outlier: 5.981A pdb=" N LYS M 66 " --> pdb=" O GLY M 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET M 70 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N SER M 51 " --> pdb=" O MET M 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA M 103 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N HIS M 99 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N LEU M 52 " --> pdb=" O MET M 97 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N MET M 97 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N ILE M 54 " --> pdb=" O GLY M 95 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N GLY M 95 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 17.053A pdb=" N ILE M 56 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 19.912A pdb=" N ILE M 93 " --> pdb=" O ILE M 56 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 84 through 86 removed outlier: 4.327A pdb=" N GLU M 109 " --> pdb=" O PHE M 129 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 149 through 156 removed outlier: 3.599A pdb=" N CYS M 153 " --> pdb=" O VAL M 264 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 236 through 237 removed outlier: 3.898A pdb=" N GLY M 253 " --> pdb=" O VAL M 169 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 175 through 176 removed outlier: 3.534A pdb=" N GLY M 209 " --> pdb=" O TYR M 199 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 181 through 184 Processing sheet with id=AF6, first strand: chain 'M' and resid 275 through 279 removed outlier: 4.052A pdb=" N LYS M 315 " --> pdb=" O LEU M 287 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 143 through 144 removed outlier: 6.855A pdb=" N PHE Q 115 " --> pdb=" O TYR Q 126 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR Q 126 " --> pdb=" O PHE Q 115 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL Q 117 " --> pdb=" O MET Q 124 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR Q 126 " --> pdb=" O PRO Q 137 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 249 through 253 removed outlier: 6.914A pdb=" N ALA Q 239 " --> pdb=" O GLY Q 231 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY Q 231 " --> pdb=" O ALA Q 239 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER Q 241 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP Q 245 " --> pdb=" O VAL Q 225 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL Q 225 " --> pdb=" O TRP Q 245 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA Q 226 " --> pdb=" O ILE Q 217 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN Q 188 " --> pdb=" O PHE Q 218 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N ALA Q 193 " --> pdb=" O PRO Q 204 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE Q 201 " --> pdb=" O LEU Q 240 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU Q 240 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.600A pdb=" N LYS C 160 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 15 through 19 removed outlier: 3.928A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS C 132 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER C 130 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 38 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR C 126 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 42 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA C 124 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 44 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR C 122 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR C 46 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER C 120 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 120 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 140 through 147 removed outlier: 4.884A pdb=" N SER C 120 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR C 46 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR C 122 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 44 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA C 124 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 42 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR C 126 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 38 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER C 130 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS C 132 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AG4, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AG5, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AG6, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AG7, first strand: chain 'C' and resid 219 through 221 Processing sheet with id=AG8, first strand: chain 'C' and resid 296 through 306 removed outlier: 4.588A pdb=" N ASP C 298 " --> pdb=" O THR C 321 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 321 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL C 315 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AH1, first strand: chain 'C' and resid 387 through 388 removed outlier: 3.517A pdb=" N TYR O 297 " --> pdb=" O HIS O 307 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'X' and resid 3 through 7 removed outlier: 3.540A pdb=" N SER X 71 " --> pdb=" O TYR X 80 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.584A pdb=" N THR X 114 " --> pdb=" O TYR X 94 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET X 34 " --> pdb=" O TYR X 50 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'W' and resid 10 through 12 removed outlier: 6.371A pdb=" N LEU W 11 " --> pdb=" O GLU W 105 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 10 through 12 removed outlier: 6.371A pdb=" N LEU W 11 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR W 97 " --> pdb=" O GLN W 90 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 17 through 19 removed outlier: 3.511A pdb=" N CYS O 28 " --> pdb=" O CYS O 19 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 74 through 79 removed outlier: 5.975A pdb=" N LYS O 66 " --> pdb=" O GLY O 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN O 53 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET O 70 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N SER O 51 " --> pdb=" O MET O 70 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA O 103 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N HIS O 99 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N LEU O 52 " --> pdb=" O MET O 97 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET O 97 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N ILE O 54 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N GLY O 95 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 17.134A pdb=" N ILE O 56 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 19.961A pdb=" N ILE O 93 " --> pdb=" O ILE O 56 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 84 through 86 removed outlier: 4.246A pdb=" N GLU O 109 " --> pdb=" O PHE O 129 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 149 through 156 Processing sheet with id=AI2, first strand: chain 'O' and resid 236 through 237 removed outlier: 4.136A pdb=" N GLY O 253 " --> pdb=" O VAL O 169 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 175 through 176 removed outlier: 3.804A pdb=" N GLY O 209 " --> pdb=" O TYR O 199 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 181 through 184 removed outlier: 3.530A pdb=" N LYS O 215 " --> pdb=" O ILE O 190 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'O' and resid 275 through 279 removed outlier: 3.889A pdb=" N LYS O 315 " --> pdb=" O LEU O 287 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'S' and resid 143 through 144 removed outlier: 6.643A pdb=" N PHE S 115 " --> pdb=" O TYR S 126 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR S 126 " --> pdb=" O PHE S 115 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL S 117 " --> pdb=" O MET S 124 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N TYR S 126 " --> pdb=" O PRO S 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU S 162 " --> pdb=" O SER S 157 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER S 157 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS S 164 " --> pdb=" O LYS S 155 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS S 155 " --> pdb=" O CYS S 164 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'S' and resid 249 through 253 removed outlier: 4.515A pdb=" N GLY S 230 " --> pdb=" O SER S 241 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL S 243 " --> pdb=" O VAL S 228 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL S 228 " --> pdb=" O VAL S 243 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N TRP S 245 " --> pdb=" O ALA S 226 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA S 226 " --> pdb=" O TRP S 245 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE S 217 " --> pdb=" O VAL S 225 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN S 188 " --> pdb=" O PHE S 218 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY S 185 " --> pdb=" O TYR S 196 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ALA S 193 " --> pdb=" O PRO S 204 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG S 200 " --> pdb=" O SER S 197 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE S 201 " --> pdb=" O LEU S 240 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.565A pdb=" N LYS D 160 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 15 through 19 removed outlier: 9.726A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET D 31 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL D 135 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU D 33 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA D 131 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 37 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA D 129 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU D 39 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA D 127 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 120 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.758A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA D 127 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU D 39 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA D 129 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 37 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA D 131 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU D 33 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL D 135 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET D 31 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AJ3, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.526A pdb=" N SER D 104 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 79 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AJ5, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AJ6, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AJ7, first strand: chain 'D' and resid 296 through 306 removed outlier: 4.293A pdb=" N ASP D 298 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL D 315 " --> pdb=" O PRO D 304 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER D 350 " --> pdb=" O TYR D 320 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AJ9, first strand: chain 'D' and resid 387 through 388 removed outlier: 3.511A pdb=" N TYR P 297 " --> pdb=" O HIS P 307 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 3 through 7 Processing sheet with id=AK2, first strand: chain 'Z' and resid 10 through 12 removed outlier: 6.243A pdb=" N GLY Z 10 " --> pdb=" O THR Z 117 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N MET Z 34 " --> pdb=" O TYR Z 50 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR Z 50 " --> pdb=" O MET Z 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP Z 36 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'Z' and resid 10 through 12 removed outlier: 6.243A pdb=" N GLY Z 10 " --> pdb=" O THR Z 117 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR Z 109 " --> pdb=" O ARG Z 98 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.763A pdb=" N VAL Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Y' and resid 10 through 12 removed outlier: 6.105A pdb=" N LEU Y 11 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'P' and resid 17 through 19 removed outlier: 3.520A pdb=" N CYS P 28 " --> pdb=" O CYS P 19 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'P' and resid 74 through 79 removed outlier: 5.898A pdb=" N LYS P 66 " --> pdb=" O GLY P 55 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET P 70 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 10.764A pdb=" N SER P 51 " --> pdb=" O MET P 70 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N HIS P 99 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU P 52 " --> pdb=" O MET P 97 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N MET P 97 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N ILE P 54 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 11.487A pdb=" N GLY P 95 " --> pdb=" O ILE P 54 " (cutoff:3.500A) removed outlier: 17.117A pdb=" N ILE P 56 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 20.000A pdb=" N ILE P 93 " --> pdb=" O ILE P 56 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'P' and resid 84 through 86 removed outlier: 4.369A pdb=" N GLU P 109 " --> pdb=" O PHE P 129 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'P' and resid 149 through 156 Processing sheet with id=AL1, first strand: chain 'P' and resid 236 through 237 removed outlier: 3.986A pdb=" N GLY P 253 " --> pdb=" O VAL P 169 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'P' and resid 175 through 176 removed outlier: 3.619A pdb=" N GLY P 209 " --> pdb=" O TYR P 199 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'P' and resid 181 through 184 removed outlier: 3.533A pdb=" N LYS P 215 " --> pdb=" O ILE P 190 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'P' and resid 275 through 279 removed outlier: 3.928A pdb=" N LYS P 315 " --> pdb=" O LEU P 287 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'T' and resid 143 through 144 removed outlier: 6.712A pdb=" N PHE T 115 " --> pdb=" O TYR T 126 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR T 126 " --> pdb=" O PHE T 115 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL T 117 " --> pdb=" O MET T 124 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N TYR T 126 " --> pdb=" O PRO T 137 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'T' and resid 249 through 253 removed outlier: 4.160A pdb=" N GLY T 230 " --> pdb=" O SER T 241 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL T 243 " --> pdb=" O VAL T 228 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL T 228 " --> pdb=" O VAL T 243 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N TRP T 245 " --> pdb=" O ALA T 226 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ALA T 226 " --> pdb=" O TRP T 245 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE T 217 " --> pdb=" O VAL T 225 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN T 188 " --> pdb=" O PHE T 218 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ALA T 193 " --> pdb=" O PRO T 204 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG T 200 " --> pdb=" O SER T 197 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE T 201 " --> pdb=" O LEU T 240 " (cutoff:3.500A) 1497 hydrogen bonds defined for protein. 3732 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: 17.62 Time building geometry restraints manager: 14.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12309 1.34 - 1.47: 9317 1.47 - 1.59: 16862 1.59 - 1.71: 0 1.71 - 1.84: 356 Bond restraints: 38844 Sorted by residual: bond pdb=" N MET Q 124 " pdb=" CA MET Q 124 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.27e-02 6.20e+03 6.00e+00 bond pdb=" N MET Z 34 " pdb=" CA MET Z 34 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.27e-02 6.20e+03 5.91e+00 bond pdb=" N CYS A 94 " pdb=" CA CYS A 94 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.23e-02 6.61e+03 5.65e+00 bond pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.46e+00 bond pdb=" CB CYS D 94 " pdb=" SG CYS D 94 " ideal model delta sigma weight residual 1.808 1.732 0.076 3.30e-02 9.18e+02 5.26e+00 ... (remaining 38839 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.73: 959 104.73 - 112.09: 19510 112.09 - 119.45: 12549 119.45 - 126.81: 19228 126.81 - 134.18: 654 Bond angle restraints: 52900 Sorted by residual: angle pdb=" C TYR A 93 " pdb=" N CYS A 94 " pdb=" CA CYS A 94 " ideal model delta sigma weight residual 122.81 115.48 7.33 1.57e+00 4.06e-01 2.18e+01 angle pdb=" CA CYS C 94 " pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 114.40 123.53 -9.13 2.30e+00 1.89e-01 1.58e+01 angle pdb=" CA ASN N 202 " pdb=" CB ASN N 202 " pdb=" CG ASN N 202 " ideal model delta sigma weight residual 112.60 116.47 -3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" CA CYS D 94 " pdb=" CB CYS D 94 " pdb=" SG CYS D 94 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" CB LYS R 221 " pdb=" CG LYS R 221 " pdb=" CD LYS R 221 " ideal model delta sigma weight residual 111.30 120.00 -8.70 2.30e+00 1.89e-01 1.43e+01 ... (remaining 52895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 21585 17.99 - 35.98: 1367 35.98 - 53.97: 403 53.97 - 71.96: 91 71.96 - 89.94: 34 Dihedral angle restraints: 23480 sinusoidal: 9264 harmonic: 14216 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 28 " pdb=" CB CYS M 28 " ideal model delta sinusoidal sigma weight residual -86.00 -174.17 88.17 1 1.00e+01 1.00e-02 9.29e+01 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 -86.00 -167.91 81.91 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS D 62 " pdb=" SG CYS D 62 " pdb=" SG CYS D 94 " pdb=" CB CYS D 94 " ideal model delta sinusoidal sigma weight residual -86.00 -161.52 75.52 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 23477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5236 0.075 - 0.150: 699 0.150 - 0.225: 16 0.225 - 0.300: 6 0.300 - 0.376: 3 Chirality restraints: 5960 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 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C1 NAG O 501 " pdb=" ND2 ASN O 263 " pdb=" C2 NAG O 501 " pdb=" O5 NAG O 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.26e+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 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 5957 not shown) Planarity restraints: 6816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 254 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.62e+01 pdb=" N PRO S 255 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO S 255 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO S 255 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 254 " 0.056 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO R 255 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO R 255 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 255 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 136 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO Q 137 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO Q 137 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO Q 137 " 0.046 5.00e-02 4.00e+02 ... (remaining 6813 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 175 2.63 - 3.20: 29483 3.20 - 3.76: 50716 3.76 - 4.33: 66645 4.33 - 4.90: 116057 Nonbonded interactions: 263076 Sorted by model distance: nonbonded pdb=" OD1 ASP O 117 " pdb=" N SER O 118 " model vdw 2.062 2.520 nonbonded pdb=" OD1 ASP M 117 " pdb=" N SER M 118 " model vdw 2.109 2.520 nonbonded pdb=" OG SER M 30 " pdb=" O ILE M 32 " model vdw 2.124 2.440 nonbonded pdb=" OG SER P 30 " pdb=" O ILE P 32 " model vdw 2.167 2.440 nonbonded pdb=" OG1 THR A 10 " pdb=" OH TYR A 15 " model vdw 2.202 2.440 ... (remaining 263071 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: 2.930 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: 11.600 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 101.120 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.380 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 0.077 38844 Z= 0.178 Angle : 0.644 12.438 52900 Z= 0.363 Chirality : 0.047 0.376 5960 Planarity : 0.005 0.150 6804 Dihedral : 13.533 89.944 14180 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.35 % Favored : 98.52 % Rotamer: Outliers : 0.26 % Allowed : 11.74 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.11), residues: 4876 helix: 1.97 (0.23), residues: 427 sheet: 1.06 (0.11), residues: 1868 loop : 0.11 (0.11), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 89 HIS 0.010 0.001 HIS O 313 PHE 0.021 0.001 PHE D 436 TYR 0.020 0.001 TYR H 50 ARG 0.009 0.000 ARG N 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 669 time to evaluate : 4.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 70 MET cc_start: 0.8151 (tpp) cc_final: 0.7810 (tpp) REVERT: A 209 GLU cc_start: 0.6865 (mp0) cc_final: 0.6563 (mp0) REVERT: A 223 ARG cc_start: 0.8485 (ttt-90) cc_final: 0.8175 (ttt-90) REVERT: V 34 MET cc_start: 0.7022 (mmm) cc_final: 0.6495 (mmm) REVERT: C 410 VAL cc_start: 0.8951 (t) cc_final: 0.8716 (p) REVERT: P 171 MET cc_start: 0.8400 (ttt) cc_final: 0.8122 (ttt) outliers start: 11 outliers final: 9 residues processed: 675 average time/residue: 0.4860 time to fit residues: 527.0210 Evaluate side-chains 650 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 641 time to evaluate : 4.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain T residue 229 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 20.0000 chunk 363 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 376 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 280 optimal weight: 6.9990 chunk 435 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 GLN L 38 GLN L 79 GLN N 26 HIS N 53 GLN N 202 ASN N 273 ASN R 111 ASN A 34 GLN A 186 ASN A 216 ASN A 222 GLN A 331 HIS A 389 ASN V 101 ASN U 38 GLN M 158 GLN M 234 ASN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN Q 190 HIS C 252 GLN ** C 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 38 GLN O 146 GLN O 313 HIS O 341 GLN S 166 GLN D 331 HIS P 62 HIS P 131 HIS P 273 ASN P 299 ASN P 302 GLN T 170 HIS T 190 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 38844 Z= 0.520 Angle : 0.809 11.705 52900 Z= 0.458 Chirality : 0.053 0.403 5960 Planarity : 0.008 0.094 6804 Dihedral : 6.016 52.433 5584 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.01 % Favored : 97.97 % Rotamer: Outliers : 2.91 % Allowed : 11.12 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 4876 helix: 2.33 (0.24), residues: 414 sheet: 1.05 (0.12), residues: 1593 loop : -1.02 (0.10), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP O 330 HIS 0.019 0.003 HIS P 99 PHE 0.027 0.003 PHE S 201 TYR 0.035 0.003 TYR A 122 ARG 0.007 0.001 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 699 time to evaluate : 4.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8056 (mtp) cc_final: 0.7739 (mtm) REVERT: B 143 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8089 (t) REVERT: B 288 THR cc_start: 0.8128 (m) cc_final: 0.7796 (p) REVERT: B 401 ASP cc_start: 0.7699 (m-30) cc_final: 0.7394 (m-30) REVERT: B 407 MET cc_start: 0.7684 (tpt) cc_final: 0.7233 (tpt) REVERT: N 165 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7635 (mt-10) REVERT: N 202 ASN cc_start: 0.8345 (t160) cc_final: 0.8095 (t0) REVERT: R 111 ASN cc_start: 0.5164 (OUTLIER) cc_final: 0.4518 (m-40) REVERT: R 161 ASP cc_start: 0.7927 (m-30) cc_final: 0.7712 (m-30) REVERT: R 229 LEU cc_start: 0.8362 (pt) cc_final: 0.8158 (pp) REVERT: A 61 LYS cc_start: 0.7754 (tttp) cc_final: 0.7488 (ttmt) REVERT: A 209 GLU cc_start: 0.7017 (mp0) cc_final: 0.6657 (mp0) REVERT: A 223 ARG cc_start: 0.8579 (ttt-90) cc_final: 0.8299 (ttt-90) REVERT: A 370 CYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6760 (m) REVERT: A 434 VAL cc_start: 0.8388 (t) cc_final: 0.8166 (p) REVERT: M 171 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8213 (ttp) REVERT: M 193 ASN cc_start: 0.8426 (m110) cc_final: 0.7871 (m110) REVERT: Q 124 MET cc_start: 0.6833 (mmm) cc_final: 0.6471 (mmp) REVERT: C 292 ASP cc_start: 0.7679 (m-30) cc_final: 0.7409 (t0) REVERT: C 319 LYS cc_start: 0.8081 (mttt) cc_final: 0.7871 (mtpt) REVERT: C 410 VAL cc_start: 0.8857 (t) cc_final: 0.8640 (p) REVERT: W 52 SER cc_start: 0.8499 (m) cc_final: 0.8292 (p) REVERT: O 165 GLU cc_start: 0.7402 (tt0) cc_final: 0.7119 (mt-10) REVERT: O 254 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7909 (ptpp) REVERT: O 255 ILE cc_start: 0.7962 (pt) cc_final: 0.7464 (mt) REVERT: O 384 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8436 (t) REVERT: S 133 LYS cc_start: 0.8285 (mttm) cc_final: 0.8068 (mmmt) REVERT: S 241 SER cc_start: 0.8406 (m) cc_final: 0.8123 (t) REVERT: S 242 VAL cc_start: 0.8705 (p) cc_final: 0.8422 (t) REVERT: D 15 TYR cc_start: 0.7687 (m-80) cc_final: 0.7481 (m-80) REVERT: D 117 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8034 (mm-30) REVERT: D 341 GLU cc_start: 0.7494 (mp0) cc_final: 0.7177 (mp0) REVERT: Y 60 SER cc_start: 0.7223 (p) cc_final: 0.6870 (m) REVERT: P 24 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7290 (mm-30) outliers start: 121 outliers final: 68 residues processed: 765 average time/residue: 0.4963 time to fit residues: 616.0394 Evaluate side-chains 728 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 654 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 356 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 111 ASN Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain V residue 101 ASN Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 254 LYS Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 365 THR Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain S residue 250 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 174 ASP Chi-restraints excluded: chain P residue 217 ILE Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 228 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 362 optimal weight: 0.9990 chunk 296 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 436 optimal weight: 0.9990 chunk 471 optimal weight: 0.9980 chunk 388 optimal weight: 0.9980 chunk 433 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 350 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 111 ASN A 34 GLN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN C 439 HIS P 299 ASN P 302 GLN T 170 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38844 Z= 0.181 Angle : 0.569 9.840 52900 Z= 0.314 Chirality : 0.045 0.337 5960 Planarity : 0.006 0.064 6804 Dihedral : 5.321 53.218 5570 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.26 % Allowed : 12.82 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.11), residues: 4876 helix: 2.48 (0.25), residues: 427 sheet: 0.71 (0.11), residues: 1922 loop : -0.99 (0.11), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 330 HIS 0.005 0.001 HIS P 99 PHE 0.016 0.001 PHE M 115 TYR 0.013 0.001 TYR V 32 ARG 0.006 0.000 ARG Q 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 676 time to evaluate : 4.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 THR cc_start: 0.8315 (p) cc_final: 0.8082 (t) REVERT: B 319 LYS cc_start: 0.7812 (mttm) cc_final: 0.7574 (mttp) REVERT: B 401 ASP cc_start: 0.7727 (m-30) cc_final: 0.7421 (m-30) REVERT: B 407 MET cc_start: 0.7222 (tpt) cc_final: 0.6668 (tpt) REVERT: N 56 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8349 (tt) REVERT: N 202 ASN cc_start: 0.8284 (t160) cc_final: 0.7993 (t0) REVERT: R 196 TYR cc_start: 0.6079 (t80) cc_final: 0.5663 (t80) REVERT: A 9 ASN cc_start: 0.8514 (t0) cc_final: 0.8072 (t0) REVERT: A 61 LYS cc_start: 0.7536 (tttp) cc_final: 0.7258 (ttmt) REVERT: A 209 GLU cc_start: 0.7035 (mp0) cc_final: 0.6710 (mp0) REVERT: A 223 ARG cc_start: 0.8516 (ttt-90) cc_final: 0.8185 (ttt-90) REVERT: A 370 CYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6551 (m) REVERT: A 374 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7746 (m) REVERT: M 87 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7091 (t) REVERT: M 171 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8081 (ttp) REVERT: M 193 ASN cc_start: 0.8299 (m110) cc_final: 0.7733 (m110) REVERT: Q 124 MET cc_start: 0.6759 (mmm) cc_final: 0.6437 (mmp) REVERT: Q 218 PHE cc_start: 0.8546 (m-80) cc_final: 0.7850 (m-80) REVERT: C 33 LEU cc_start: 0.7969 (tp) cc_final: 0.7753 (tp) REVERT: C 347 GLU cc_start: 0.8568 (tt0) cc_final: 0.8327 (tt0) REVERT: X 49 SER cc_start: 0.7361 (m) cc_final: 0.7136 (p) REVERT: O 87 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7358 (t) REVERT: O 254 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7796 (ptpp) REVERT: O 255 ILE cc_start: 0.7833 (pt) cc_final: 0.7339 (mt) REVERT: O 384 THR cc_start: 0.8773 (m) cc_final: 0.8437 (t) REVERT: S 133 LYS cc_start: 0.8210 (mttm) cc_final: 0.8006 (mmmt) REVERT: Y 60 SER cc_start: 0.7156 (p) cc_final: 0.6807 (m) REVERT: P 24 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7244 (mm-30) REVERT: P 52 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7878 (pp) REVERT: T 229 LEU cc_start: 0.8885 (pt) cc_final: 0.8625 (pp) outliers start: 94 outliers final: 52 residues processed: 725 average time/residue: 0.4956 time to fit residues: 578.8106 Evaluate side-chains 714 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 654 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 24 GLU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 153 CYS Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain R residue 260 GLU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 410 PHE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 254 LYS Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 174 ASP Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 228 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 6.9990 chunk 328 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 293 optimal weight: 0.0570 chunk 438 optimal weight: 2.9990 chunk 463 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 415 optimal weight: 0.0870 chunk 125 optimal weight: 3.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN R 111 ASN M 53 GLN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN C 353 GLN O 53 GLN O 313 HIS Y 38 GLN T 170 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38844 Z= 0.267 Angle : 0.611 12.001 52900 Z= 0.337 Chirality : 0.046 0.356 5960 Planarity : 0.006 0.059 6804 Dihedral : 5.355 52.203 5564 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.83 % Allowed : 13.45 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 4876 helix: 2.55 (0.26), residues: 419 sheet: 0.72 (0.12), residues: 1812 loop : -1.19 (0.11), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 330 HIS 0.010 0.002 HIS P 99 PHE 0.018 0.002 PHE C 436 TYR 0.022 0.002 TYR C 122 ARG 0.005 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 682 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.7982 (mtp) cc_final: 0.7743 (mtm) REVERT: B 134 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7837 (ttp-170) REVERT: B 288 THR cc_start: 0.8015 (m) cc_final: 0.7732 (p) REVERT: B 401 ASP cc_start: 0.7786 (m-30) cc_final: 0.7469 (m-30) REVERT: B 407 MET cc_start: 0.7199 (tpt) cc_final: 0.6608 (tpt) REVERT: N 56 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8374 (tt) REVERT: N 165 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7606 (mt-10) REVERT: N 171 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8095 (ttp) REVERT: N 202 ASN cc_start: 0.8298 (t160) cc_final: 0.7999 (t0) REVERT: R 196 TYR cc_start: 0.6065 (t80) cc_final: 0.5757 (t80) REVERT: A 61 LYS cc_start: 0.7583 (tttp) cc_final: 0.7329 (ttmt) REVERT: A 112 GLU cc_start: 0.7792 (tp30) cc_final: 0.7526 (tp30) REVERT: A 209 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: A 223 ARG cc_start: 0.8539 (ttt-90) cc_final: 0.8211 (ttt-90) REVERT: A 370 CYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6377 (m) REVERT: A 374 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7812 (m) REVERT: M 19 CYS cc_start: 0.7722 (t) cc_final: 0.7363 (t) REVERT: M 87 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7102 (t) REVERT: M 171 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8112 (ttp) REVERT: M 193 ASN cc_start: 0.8355 (m110) cc_final: 0.7938 (m110) REVERT: Q 124 MET cc_start: 0.6682 (mmm) cc_final: 0.6476 (mmp) REVERT: Q 218 PHE cc_start: 0.8597 (m-80) cc_final: 0.8003 (m-80) REVERT: C 33 LEU cc_start: 0.8029 (tp) cc_final: 0.7785 (tp) REVERT: C 347 GLU cc_start: 0.8522 (tt0) cc_final: 0.8276 (tt0) REVERT: X 49 SER cc_start: 0.7420 (m) cc_final: 0.7215 (p) REVERT: W 52 SER cc_start: 0.8439 (m) cc_final: 0.8221 (p) REVERT: O 87 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7353 (p) REVERT: O 165 GLU cc_start: 0.7382 (tt0) cc_final: 0.7107 (mt-10) REVERT: O 178 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7481 (mtp85) REVERT: O 255 ILE cc_start: 0.7891 (pt) cc_final: 0.7382 (mt) REVERT: O 263 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7298 (m-40) REVERT: O 384 THR cc_start: 0.8764 (m) cc_final: 0.8476 (t) REVERT: S 241 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.7894 (p) REVERT: S 242 VAL cc_start: 0.8693 (p) cc_final: 0.8415 (t) REVERT: Y 60 SER cc_start: 0.7223 (p) cc_final: 0.6897 (m) REVERT: P 24 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7590 (mt-10) REVERT: P 52 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7852 (pp) REVERT: T 229 LEU cc_start: 0.8857 (pt) cc_final: 0.8606 (pp) outliers start: 118 outliers final: 88 residues processed: 745 average time/residue: 0.4920 time to fit residues: 592.3183 Evaluate side-chains 760 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 661 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 208 GLU Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain R residue 132 ASP Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 410 PHE Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 124 MET Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 241 SER Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 174 ASP Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 0.9990 chunk 263 optimal weight: 0.4980 chunk 6 optimal weight: 9.9990 chunk 345 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 395 optimal weight: 5.9990 chunk 320 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 416 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN A 175 ASN V 13 GLN V 101 ASN M 158 GLN M 302 GLN Q 166 GLN O 131 HIS O 313 HIS O 341 GLN D 230 HIS P 123 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 38844 Z= 0.338 Angle : 0.658 11.533 52900 Z= 0.364 Chirality : 0.048 0.372 5960 Planarity : 0.007 0.065 6804 Dihedral : 5.645 59.775 5564 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.58 % Allowed : 13.33 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 4876 helix: 2.23 (0.25), residues: 427 sheet: 0.70 (0.12), residues: 1690 loop : -1.54 (0.10), residues: 2759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 330 HIS 0.013 0.002 HIS P 99 PHE 0.020 0.002 PHE C 436 TYR 0.027 0.002 TYR C 122 ARG 0.009 0.000 ARG M 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 690 time to evaluate : 4.280 Fit side-chains revert: symmetry clash REVERT: B 88 MET cc_start: 0.8024 (mtp) cc_final: 0.7778 (mtm) REVERT: B 133 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8178 (mt) REVERT: B 134 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7819 (ttp-170) REVERT: B 196 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7474 (mmt-90) REVERT: B 288 THR cc_start: 0.8121 (m) cc_final: 0.7736 (p) REVERT: B 401 ASP cc_start: 0.7819 (m-30) cc_final: 0.7476 (m-30) REVERT: B 407 MET cc_start: 0.7358 (tpt) cc_final: 0.6749 (tpt) REVERT: N 56 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8395 (tt) REVERT: N 165 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7661 (mt-10) REVERT: N 171 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8116 (ttp) REVERT: N 202 ASN cc_start: 0.8310 (t160) cc_final: 0.8000 (t0) REVERT: N 372 SER cc_start: 0.7890 (p) cc_final: 0.7571 (m) REVERT: A 61 LYS cc_start: 0.7779 (tttp) cc_final: 0.7532 (ttmt) REVERT: A 209 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: A 223 ARG cc_start: 0.8549 (ttt-90) cc_final: 0.8259 (ttt-90) REVERT: M 87 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6957 (t) REVERT: M 171 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8188 (ttp) REVERT: M 193 ASN cc_start: 0.8441 (m110) cc_final: 0.8043 (m110) REVERT: Q 124 MET cc_start: 0.6624 (mmm) cc_final: 0.6413 (mmp) REVERT: Q 218 PHE cc_start: 0.8620 (m-80) cc_final: 0.8024 (m-80) REVERT: C 13 VAL cc_start: 0.8288 (t) cc_final: 0.7880 (m) REVERT: C 347 GLU cc_start: 0.8494 (tt0) cc_final: 0.8256 (tt0) REVERT: C 385 ASP cc_start: 0.7802 (m-30) cc_final: 0.7408 (m-30) REVERT: W 52 SER cc_start: 0.8472 (m) cc_final: 0.8235 (p) REVERT: O 87 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7510 (p) REVERT: O 127 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.7888 (m170) REVERT: O 165 GLU cc_start: 0.7379 (tt0) cc_final: 0.7114 (mt-10) REVERT: O 178 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7465 (mtp85) REVERT: O 255 ILE cc_start: 0.7931 (pt) cc_final: 0.7406 (mt) REVERT: O 384 THR cc_start: 0.8766 (m) cc_final: 0.8488 (t) REVERT: S 177 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7787 (mmmm) REVERT: S 241 SER cc_start: 0.8437 (m) cc_final: 0.7927 (p) REVERT: S 242 VAL cc_start: 0.8694 (p) cc_final: 0.8447 (t) REVERT: D 130 SER cc_start: 0.8776 (p) cc_final: 0.8464 (m) REVERT: Y 4 MET cc_start: 0.4650 (OUTLIER) cc_final: 0.4084 (mtm) REVERT: P 52 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7873 (pp) REVERT: T 229 LEU cc_start: 0.8825 (pt) cc_final: 0.8566 (pp) outliers start: 149 outliers final: 106 residues processed: 766 average time/residue: 0.4745 time to fit residues: 585.5119 Evaluate side-chains 771 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 654 time to evaluate : 4.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 153 CYS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 208 GLU Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain R residue 132 ASP Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 357 LEU Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 228 VAL Chi-restraints excluded: chain S residue 249 ILE 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 228 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 388 MET Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 3.9990 chunk 417 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 272 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 464 optimal weight: 7.9990 chunk 385 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS N 341 GLN A 175 ASN V 101 ASN M 53 GLN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN O 158 GLN D 375 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 38844 Z= 0.159 Angle : 0.541 11.642 52900 Z= 0.292 Chirality : 0.044 0.314 5960 Planarity : 0.006 0.052 6804 Dihedral : 5.177 59.240 5564 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.33 % Allowed : 15.18 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 4876 helix: 2.61 (0.26), residues: 431 sheet: 0.65 (0.12), residues: 1832 loop : -1.39 (0.11), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 110 HIS 0.005 0.001 HIS D 375 PHE 0.020 0.001 PHE A 436 TYR 0.010 0.001 TYR B 242 ARG 0.007 0.000 ARG M 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 681 time to evaluate : 4.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.7972 (mtp) cc_final: 0.7741 (mtm) REVERT: B 130 SER cc_start: 0.8589 (p) cc_final: 0.8287 (m) REVERT: B 134 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7806 (ttp-170) REVERT: B 196 ARG cc_start: 0.7920 (mmt-90) cc_final: 0.7479 (mmt-90) REVERT: B 288 THR cc_start: 0.8112 (m) cc_final: 0.7841 (p) REVERT: B 401 ASP cc_start: 0.7832 (m-30) cc_final: 0.7516 (m-30) REVERT: B 407 MET cc_start: 0.6781 (tpt) cc_final: 0.6055 (tpt) REVERT: N 70 MET cc_start: 0.8094 (tpp) cc_final: 0.7884 (tpp) REVERT: N 202 ASN cc_start: 0.8282 (t160) cc_final: 0.7979 (t0) REVERT: A 9 ASN cc_start: 0.8590 (t0) cc_final: 0.8031 (t0) REVERT: A 61 LYS cc_start: 0.7525 (tttp) cc_final: 0.7293 (ttmt) REVERT: A 209 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: M 56 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8433 (tt) REVERT: M 87 THR cc_start: 0.6974 (OUTLIER) cc_final: 0.6674 (t) REVERT: M 193 ASN cc_start: 0.8365 (m110) cc_final: 0.7923 (m110) REVERT: M 267 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7410 (ttm170) REVERT: Q 218 PHE cc_start: 0.8551 (m-80) cc_final: 0.8098 (m-80) REVERT: C 347 GLU cc_start: 0.8450 (tt0) cc_final: 0.8167 (tt0) REVERT: C 385 ASP cc_start: 0.7575 (m-30) cc_final: 0.7206 (m-30) REVERT: X 70 ILE cc_start: 0.7509 (tt) cc_final: 0.7222 (pt) REVERT: W 52 SER cc_start: 0.8431 (m) cc_final: 0.8196 (p) REVERT: O 178 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7453 (mtp85) REVERT: O 402 LEU cc_start: 0.7759 (mt) cc_final: 0.7528 (mt) REVERT: S 241 SER cc_start: 0.8422 (m) cc_final: 0.8078 (p) REVERT: D 130 SER cc_start: 0.8797 (p) cc_final: 0.8454 (m) REVERT: D 156 VAL cc_start: 0.7625 (t) cc_final: 0.7353 (p) REVERT: D 428 LEU cc_start: 0.8429 (tp) cc_final: 0.8221 (tp) REVERT: Y 4 MET cc_start: 0.4676 (OUTLIER) cc_final: 0.4054 (mtm) REVERT: Y 60 SER cc_start: 0.7277 (p) cc_final: 0.6962 (m) REVERT: P 52 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7828 (pp) REVERT: T 229 LEU cc_start: 0.8830 (pt) cc_final: 0.8574 (pp) outliers start: 97 outliers final: 65 residues processed: 734 average time/residue: 0.4913 time to fit residues: 586.1575 Evaluate side-chains 731 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 660 time to evaluate : 4.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 208 GLU Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 260 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 267 ARG Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 264 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 390 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 462 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN O 313 HIS D 375 HIS P 224 GLN P 299 ASN T 170 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 38844 Z= 0.462 Angle : 0.721 13.994 52900 Z= 0.396 Chirality : 0.051 0.364 5960 Planarity : 0.007 0.066 6804 Dihedral : 5.739 55.432 5564 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.05 % Allowed : 15.20 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.11), residues: 4876 helix: 2.21 (0.25), residues: 419 sheet: 0.60 (0.12), residues: 1700 loop : -1.75 (0.10), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 189 HIS 0.012 0.002 HIS P 99 PHE 0.023 0.003 PHE S 201 TYR 0.034 0.002 TYR C 122 ARG 0.008 0.001 ARG T 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 672 time to evaluate : 4.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8038 (mtp) cc_final: 0.7802 (mtm) REVERT: B 130 SER cc_start: 0.8677 (p) cc_final: 0.8356 (m) REVERT: B 133 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8227 (mt) REVERT: B 134 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7889 (ttp-170) REVERT: B 196 ARG cc_start: 0.7998 (mmt-90) cc_final: 0.7567 (mmt-90) REVERT: B 288 THR cc_start: 0.8237 (m) cc_final: 0.7945 (p) REVERT: B 401 ASP cc_start: 0.7870 (m-30) cc_final: 0.7573 (m-30) REVERT: B 407 MET cc_start: 0.7435 (tpt) cc_final: 0.6849 (tpt) REVERT: N 165 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7688 (mt-10) REVERT: N 171 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8139 (ttp) REVERT: N 202 ASN cc_start: 0.8302 (t160) cc_final: 0.8011 (t0) REVERT: N 291 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7171 (p-80) REVERT: N 372 SER cc_start: 0.7861 (p) cc_final: 0.7588 (m) REVERT: R 161 ASP cc_start: 0.8020 (m-30) cc_final: 0.7740 (m-30) REVERT: A 61 LYS cc_start: 0.7818 (tttp) cc_final: 0.7550 (ttmt) REVERT: A 209 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: A 273 VAL cc_start: 0.8257 (t) cc_final: 0.7976 (m) REVERT: M 19 CYS cc_start: 0.7750 (t) cc_final: 0.7471 (t) REVERT: M 171 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8164 (ttp) REVERT: M 193 ASN cc_start: 0.8514 (m110) cc_final: 0.8125 (m110) REVERT: M 267 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7703 (ttm170) REVERT: Q 218 PHE cc_start: 0.8633 (m-80) cc_final: 0.7997 (m-80) REVERT: C 13 VAL cc_start: 0.8298 (t) cc_final: 0.7914 (m) REVERT: C 112 GLU cc_start: 0.8300 (tp30) cc_final: 0.8063 (tp30) REVERT: C 385 ASP cc_start: 0.7866 (m-30) cc_final: 0.7503 (m-30) REVERT: W 52 SER cc_start: 0.8509 (m) cc_final: 0.8297 (p) REVERT: O 127 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7883 (m170) REVERT: O 165 GLU cc_start: 0.7421 (tt0) cc_final: 0.7146 (mt-10) REVERT: S 124 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7477 (mmp) REVERT: S 241 SER cc_start: 0.8528 (m) cc_final: 0.7970 (p) REVERT: S 242 VAL cc_start: 0.8701 (p) cc_final: 0.8439 (t) REVERT: D 130 SER cc_start: 0.8802 (p) cc_final: 0.8461 (m) REVERT: Y 4 MET cc_start: 0.4659 (OUTLIER) cc_final: 0.4055 (mtm) REVERT: Y 60 SER cc_start: 0.7442 (p) cc_final: 0.7188 (m) REVERT: P 52 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7836 (pp) REVERT: T 229 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8630 (pt) outliers start: 127 outliers final: 95 residues processed: 742 average time/residue: 0.4846 time to fit residues: 578.2499 Evaluate side-chains 765 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 659 time to evaluate : 4.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 267 ARG Chi-restraints excluded: chain M residue 382 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 295 SER 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 427 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 357 LEU Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 124 MET Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 388 MET Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 229 LEU Chi-restraints excluded: chain T residue 242 VAL Chi-restraints excluded: chain T residue 247 LYS Chi-restraints excluded: chain T residue 249 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 276 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 315 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 363 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN C 349 ASN O 313 HIS D 375 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 38844 Z= 0.268 Angle : 0.623 14.057 52900 Z= 0.340 Chirality : 0.047 0.411 5960 Planarity : 0.006 0.061 6804 Dihedral : 5.534 56.474 5564 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.83 % Allowed : 15.78 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 4876 helix: 2.25 (0.25), residues: 431 sheet: 0.68 (0.12), residues: 1694 loop : -1.78 (0.10), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 330 HIS 0.009 0.001 HIS P 99 PHE 0.022 0.002 PHE C 436 TYR 0.020 0.002 TYR C 122 ARG 0.009 0.000 ARG Q 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 670 time to evaluate : 4.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8022 (mtp) cc_final: 0.7777 (mtm) REVERT: B 130 SER cc_start: 0.8688 (p) cc_final: 0.8390 (m) REVERT: B 133 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8172 (mt) REVERT: B 134 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7827 (ttp-170) REVERT: B 196 ARG cc_start: 0.7989 (mmt-90) cc_final: 0.7520 (mmt-90) REVERT: B 288 THR cc_start: 0.8202 (m) cc_final: 0.7848 (p) REVERT: B 290 VAL cc_start: 0.7896 (p) cc_final: 0.7690 (t) REVERT: B 407 MET cc_start: 0.7264 (tpt) cc_final: 0.6651 (tpt) REVERT: N 56 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8393 (tt) REVERT: N 165 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7641 (mt-10) REVERT: N 171 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8108 (ttp) REVERT: N 202 ASN cc_start: 0.8307 (t160) cc_final: 0.8016 (t0) REVERT: N 291 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7051 (p-80) REVERT: N 372 SER cc_start: 0.7828 (p) cc_final: 0.7559 (m) REVERT: A 61 LYS cc_start: 0.7742 (tttp) cc_final: 0.7491 (ttmt) REVERT: A 209 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: M 19 CYS cc_start: 0.7640 (t) cc_final: 0.7338 (t) REVERT: M 193 ASN cc_start: 0.8477 (m110) cc_final: 0.8127 (m110) REVERT: M 267 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7449 (ttm170) REVERT: Q 218 PHE cc_start: 0.8589 (m-80) cc_final: 0.8013 (m-80) REVERT: C 13 VAL cc_start: 0.8233 (t) cc_final: 0.7839 (m) REVERT: C 112 GLU cc_start: 0.8246 (tp30) cc_final: 0.8013 (tp30) REVERT: C 385 ASP cc_start: 0.7796 (m-30) cc_final: 0.7427 (m-30) REVERT: X 70 ILE cc_start: 0.7524 (tt) cc_final: 0.7167 (pt) REVERT: W 52 SER cc_start: 0.8485 (m) cc_final: 0.8275 (p) REVERT: O 127 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7818 (m170) REVERT: O 165 GLU cc_start: 0.7404 (tt0) cc_final: 0.7143 (mt-10) REVERT: S 124 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7567 (mmp) REVERT: S 228 VAL cc_start: 0.8813 (p) cc_final: 0.8598 (m) REVERT: S 241 SER cc_start: 0.8562 (m) cc_final: 0.8015 (p) REVERT: D 130 SER cc_start: 0.8798 (p) cc_final: 0.8483 (m) REVERT: Y 4 MET cc_start: 0.4654 (OUTLIER) cc_final: 0.4067 (mtm) REVERT: Y 60 SER cc_start: 0.7441 (p) cc_final: 0.7187 (m) REVERT: P 52 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7805 (pp) REVERT: T 229 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8563 (pp) outliers start: 118 outliers final: 97 residues processed: 737 average time/residue: 0.4949 time to fit residues: 592.7494 Evaluate side-chains 768 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 660 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 208 GLU Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 267 ARG Chi-restraints excluded: chain M residue 382 VAL Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 186 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain O residue 43 ASP Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 255 ILE Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 357 LEU Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 124 MET Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 388 MET Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 229 LEU Chi-restraints excluded: chain T residue 242 VAL Chi-restraints excluded: chain T residue 247 LYS Chi-restraints excluded: chain T residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 30.0000 chunk 443 optimal weight: 1.9990 chunk 404 optimal weight: 8.9990 chunk 431 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 389 optimal weight: 1.9990 chunk 407 optimal weight: 20.0000 chunk 429 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN M 53 GLN M 158 GLN M 299 ASN M 302 GLN C 349 ASN O 313 HIS D 375 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 38844 Z= 0.525 Angle : 0.787 21.929 52900 Z= 0.434 Chirality : 0.053 0.426 5960 Planarity : 0.008 0.074 6804 Dihedral : 6.034 56.016 5564 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.82 % Favored : 94.16 % Rotamer: Outliers : 3.22 % Allowed : 15.73 % Favored : 81.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.11), residues: 4876 helix: 1.81 (0.25), residues: 430 sheet: 0.45 (0.12), residues: 1684 loop : -2.10 (0.10), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP T 189 HIS 0.016 0.003 HIS P 99 PHE 0.029 0.003 PHE R 201 TYR 0.037 0.003 TYR C 122 ARG 0.008 0.001 ARG T 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 691 time to evaluate : 4.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.8021 (mtp) cc_final: 0.7788 (mtm) REVERT: B 130 SER cc_start: 0.8666 (p) cc_final: 0.8369 (m) REVERT: B 134 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7932 (ttp-170) REVERT: B 288 THR cc_start: 0.8233 (m) cc_final: 0.8010 (p) REVERT: B 289 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.7393 (mtm-85) REVERT: B 290 VAL cc_start: 0.7943 (p) cc_final: 0.7735 (t) REVERT: B 311 ASP cc_start: 0.7585 (t0) cc_final: 0.7319 (t0) REVERT: B 401 ASP cc_start: 0.7902 (m-30) cc_final: 0.7578 (m-30) REVERT: B 407 MET cc_start: 0.7668 (tpt) cc_final: 0.7183 (tpt) REVERT: N 165 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7711 (mt-10) REVERT: N 171 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8162 (ttp) REVERT: N 202 ASN cc_start: 0.8291 (t160) cc_final: 0.8000 (t0) REVERT: N 291 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7229 (p-80) REVERT: N 372 SER cc_start: 0.7876 (p) cc_final: 0.7663 (m) REVERT: R 161 ASP cc_start: 0.8056 (m-30) cc_final: 0.7771 (m-30) REVERT: A 61 LYS cc_start: 0.7858 (tttp) cc_final: 0.7564 (ttmt) REVERT: A 209 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: A 273 VAL cc_start: 0.8339 (t) cc_final: 0.8100 (m) REVERT: M 19 CYS cc_start: 0.7760 (t) cc_final: 0.7544 (t) REVERT: M 87 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6663 (p) REVERT: M 171 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8223 (ttp) REVERT: M 193 ASN cc_start: 0.8572 (m110) cc_final: 0.8291 (m110) REVERT: M 267 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7538 (ttm170) REVERT: Q 218 PHE cc_start: 0.8648 (m-80) cc_final: 0.8071 (m-80) REVERT: C 13 VAL cc_start: 0.8348 (t) cc_final: 0.7986 (m) REVERT: C 112 GLU cc_start: 0.8293 (tp30) cc_final: 0.8078 (tp30) REVERT: C 385 ASP cc_start: 0.7932 (m-30) cc_final: 0.7604 (m-30) REVERT: O 127 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.7969 (m170) REVERT: O 165 GLU cc_start: 0.7498 (tt0) cc_final: 0.7237 (mt-10) REVERT: O 366 MET cc_start: 0.7416 (mpp) cc_final: 0.6962 (mpp) REVERT: O 384 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8512 (p) REVERT: S 124 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7574 (mmp) REVERT: S 228 VAL cc_start: 0.8869 (p) cc_final: 0.8642 (m) REVERT: S 241 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.7972 (p) REVERT: D 69 LYS cc_start: 0.8272 (mmtt) cc_final: 0.8051 (mmtt) REVERT: D 130 SER cc_start: 0.8814 (p) cc_final: 0.8475 (m) REVERT: Y 4 MET cc_start: 0.4888 (OUTLIER) cc_final: 0.4289 (mtm) REVERT: Y 60 SER cc_start: 0.7569 (p) cc_final: 0.7352 (m) REVERT: P 52 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7699 (pp) REVERT: P 61 SER cc_start: 0.8279 (t) cc_final: 0.7882 (p) REVERT: P 119 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.8072 (mtt90) REVERT: T 182 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8299 (mtpp) outliers start: 134 outliers final: 107 residues processed: 766 average time/residue: 0.5112 time to fit residues: 635.2352 Evaluate side-chains 784 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 665 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 356 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 112 ASP Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 267 ARG Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 382 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain O residue 43 ASP Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 357 LEU Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 124 MET Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 241 SER Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 388 MET Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 148 ASP Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 242 VAL Chi-restraints excluded: chain T residue 247 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 6.9990 chunk 455 optimal weight: 0.9980 chunk 278 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 316 optimal weight: 0.5980 chunk 478 optimal weight: 0.7980 chunk 440 optimal weight: 4.9990 chunk 380 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 294 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN M 158 GLN M 299 ASN M 302 GLN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 299 ASN P 127 HIS P 299 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 38844 Z= 0.170 Angle : 0.590 15.178 52900 Z= 0.318 Chirality : 0.046 0.405 5960 Planarity : 0.006 0.058 6804 Dihedral : 5.451 58.981 5564 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.07 % Allowed : 17.22 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.82 (0.12), residues: 4876 helix: 2.34 (0.26), residues: 431 sheet: 0.45 (0.12), residues: 1821 loop : -1.88 (0.11), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 89 HIS 0.004 0.001 HIS D 107 PHE 0.023 0.001 PHE A 436 TYR 0.017 0.001 TYR H 104 ARG 0.010 0.000 ARG M 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 697 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 MET cc_start: 0.7968 (mtp) cc_final: 0.7756 (mtm) REVERT: B 130 SER cc_start: 0.8593 (p) cc_final: 0.8331 (m) REVERT: B 134 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7767 (ttp-170) REVERT: B 196 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7562 (mmt-90) REVERT: B 211 LYS cc_start: 0.8176 (mttt) cc_final: 0.7910 (mttt) REVERT: B 288 THR cc_start: 0.8209 (m) cc_final: 0.7869 (p) REVERT: B 290 VAL cc_start: 0.7896 (p) cc_final: 0.7696 (t) REVERT: B 407 MET cc_start: 0.7097 (tpt) cc_final: 0.6472 (tpt) REVERT: N 70 MET cc_start: 0.7952 (tpp) cc_final: 0.7748 (tpp) REVERT: N 202 ASN cc_start: 0.8292 (t160) cc_final: 0.8000 (t0) REVERT: N 291 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.6830 (p-80) REVERT: N 372 SER cc_start: 0.7801 (p) cc_final: 0.7546 (m) REVERT: R 213 SER cc_start: 0.8352 (p) cc_final: 0.7496 (m) REVERT: A 9 ASN cc_start: 0.8554 (t0) cc_final: 0.8039 (t0) REVERT: A 61 LYS cc_start: 0.7646 (tttp) cc_final: 0.7382 (ttmt) REVERT: A 209 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: M 21 ASP cc_start: 0.8455 (t0) cc_final: 0.8207 (t70) REVERT: M 171 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7914 (ttp) REVERT: M 193 ASN cc_start: 0.8453 (m110) cc_final: 0.8194 (m110) REVERT: M 224 GLN cc_start: 0.7500 (mm-40) cc_final: 0.6925 (mm-40) REVERT: M 264 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7863 (m) REVERT: Q 218 PHE cc_start: 0.8563 (m-80) cc_final: 0.7983 (m-80) REVERT: C 13 VAL cc_start: 0.8155 (t) cc_final: 0.7801 (m) REVERT: C 385 ASP cc_start: 0.7753 (m-30) cc_final: 0.7421 (m-30) REVERT: C 430 VAL cc_start: 0.8385 (t) cc_final: 0.7955 (t) REVERT: X 70 ILE cc_start: 0.7491 (tt) cc_final: 0.7168 (pt) REVERT: O 127 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7469 (m170) REVERT: O 366 MET cc_start: 0.7129 (mpp) cc_final: 0.6762 (mpp) REVERT: S 124 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7575 (mmp) REVERT: S 241 SER cc_start: 0.8563 (m) cc_final: 0.8151 (p) REVERT: D 130 SER cc_start: 0.8798 (p) cc_final: 0.8470 (m) REVERT: D 428 LEU cc_start: 0.8475 (tp) cc_final: 0.8273 (tp) REVERT: Y 4 MET cc_start: 0.4669 (OUTLIER) cc_final: 0.4107 (mtm) REVERT: Y 60 SER cc_start: 0.7462 (p) cc_final: 0.7246 (m) REVERT: P 61 SER cc_start: 0.8152 (t) cc_final: 0.7744 (p) REVERT: P 400 TYR cc_start: 0.8572 (m-80) cc_final: 0.8301 (m-80) REVERT: T 229 LEU cc_start: 0.8923 (pt) cc_final: 0.8652 (pp) outliers start: 86 outliers final: 67 residues processed: 743 average time/residue: 0.4777 time to fit residues: 575.8150 Evaluate side-chains 750 residues out of total 4164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 676 time to evaluate : 4.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 260 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 124 MET Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 179 THR Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 112 THR Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain P residue 255 ILE 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 T residue 148 ASP Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 6.9990 chunk 405 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 351 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 381 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 391 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN M 158 GLN C 349 ASN ** O 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS P 299 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.141219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109304 restraints weight = 59933.883| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.34 r_work: 0.3203 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 38844 Z= 0.311 Angle : 0.656 15.417 52900 Z= 0.356 Chirality : 0.048 0.393 5960 Planarity : 0.007 0.061 6804 Dihedral : 5.554 58.056 5564 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.16 % Allowed : 17.41 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.89 (0.11), residues: 4876 helix: 2.25 (0.26), residues: 431 sheet: 0.52 (0.12), residues: 1754 loop : -1.97 (0.10), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 330 HIS 0.011 0.002 HIS P 99 PHE 0.021 0.002 PHE C 436 TYR 0.025 0.002 TYR C 122 ARG 0.009 0.000 ARG M 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10919.57 seconds wall clock time: 195 minutes 51.34 seconds (11751.34 seconds total)