Starting phenix.real_space_refine on Tue Apr 16 07:34:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwx_27765/04_2024/8dwx_27765.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwx_27765/04_2024/8dwx_27765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwx_27765/04_2024/8dwx_27765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwx_27765/04_2024/8dwx_27765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwx_27765/04_2024/8dwx_27765.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwx_27765/04_2024/8dwx_27765.pdb" } resolution = 3.27 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= 0.047 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 24116 2.51 5 N 6556 2.21 5 O 7296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B ASP 281": "OD1" <-> "OD2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "C TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C ASP 284": "OD1" <-> "OD2" Residue "C ASP 343": "OD1" <-> "OD2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D GLU 112": "OE1" <-> "OE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D ASP 385": "OD1" <-> "OD2" Residue "D ASP 401": "OD1" <-> "OD2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 24": "OE1" <-> "OE2" Residue "M ASP 43": "OD1" <-> "OD2" Residue "M ASP 60": "OD1" <-> "OD2" Residue "M ASP 77": "OD1" <-> "OD2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M GLU 166": "OE1" <-> "OE2" Residue "M ASP 174": "OD1" <-> "OD2" Residue "M ASP 177": "OD1" <-> "OD2" Residue "M TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 401": "OE1" <-> "OE2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N ASP 59": "OD1" <-> "OD2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N ASP 223": "OD1" <-> "OD2" Residue "N TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 290": "OD1" <-> "OD2" Residue "N GLU 303": "OE1" <-> "OE2" Residue "N TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 21": "OD1" <-> "OD2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O GLU 109": "OE1" <-> "OE2" Residue "O GLU 247": "OE1" <-> "OE2" Residue "O ASP 290": "OD1" <-> "OD2" Residue "O GLU 324": "OE1" <-> "OE2" Residue "P ASP 21": "OD1" <-> "OD2" Residue "P GLU 40": "OE1" <-> "OE2" Residue "P ASP 63": "OD1" <-> "OD2" Residue "P GLU 79": "OE1" <-> "OE2" Residue "P GLU 132": "OE1" <-> "OE2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P ASP 174": "OD1" <-> "OD2" Residue "P TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 161": "OD1" <-> "OD2" Residue "S PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 256": "OE1" <-> "OE2" Residue "T PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38228 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "M" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "N" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "O" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "P" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "Q" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "R" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "S" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "T" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "U" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "X" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "W" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "Z" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "Y" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 18.95, per 1000 atoms: 0.50 Number of scatterers: 38228 At special positions: 0 Unit cell: (186.76, 221.56, 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 7296 8.00 N 6556 7.00 C 24116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 125 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 28 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 105 " distance=2.03 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 266 " distance=2.06 Simple disulfide: pdb=" SG CYS M 201 " - pdb=" SG CYS M 225 " distance=2.03 Simple disulfide: pdb=" SG CYS M 203 " - pdb=" SG CYS M 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 396 " - pdb=" SG CYS M 417 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 125 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 28 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 105 " distance=2.03 Simple disulfide: pdb=" SG CYS N 153 " - pdb=" SG CYS N 266 " distance=2.05 Simple disulfide: pdb=" SG CYS N 201 " - pdb=" SG CYS N 225 " distance=2.03 Simple disulfide: pdb=" SG CYS N 203 " - pdb=" SG CYS N 220 " distance=2.03 Simple disulfide: pdb=" SG CYS N 396 " - pdb=" SG CYS N 417 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 125 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 28 " distance=2.03 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 105 " distance=2.03 Simple disulfide: pdb=" SG CYS O 153 " - pdb=" SG CYS O 266 " distance=2.03 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 P 19 " - pdb=" SG CYS P 125 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 225 " distance=2.03 Simple disulfide: pdb=" SG CYS P 203 " - pdb=" SG CYS P 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 396 " - pdb=" SG CYS P 417 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 110 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 97 " distance=2.03 Simple disulfide: pdb=" SG CYS V 105 " - pdb=" SG CYS V 110 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 97 " distance=2.03 Simple disulfide: pdb=" SG CYS X 105 " - pdb=" SG CYS X 110 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 97 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 105 " - pdb=" SG CYS Z 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " 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: 13.42 Conformation dependent library (CDL) restraints added in 7.1 seconds 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9168 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 116 sheets defined 12.5% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.83 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.643A pdb=" N LYS A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.852A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.540A pdb=" N THR A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.745A pdb=" N ALA A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 439 removed outlier: 3.625A pdb=" N VAL A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.612A pdb=" N LYS B 115 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.881A pdb=" N TYR B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.699A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.569A pdb=" N ALA B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 439 removed outlier: 3.565A pdb=" N TRP B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.742A pdb=" N LYS C 115 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 4.091A pdb=" N TYR C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.621A pdb=" N THR C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.595A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.565A pdb=" N ALA C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 439 removed outlier: 3.613A pdb=" N TRP C 409 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 427 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.686A pdb=" N LYS D 115 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.899A pdb=" N TYR D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 246 " --> pdb=" O TYR D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.712A pdb=" N THR D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 removed outlier: 3.597A pdb=" N ALA D 286 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 287 " --> pdb=" O ASP D 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 283 through 287' Processing helix chain 'D' and resid 403 through 439 removed outlier: 3.691A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 427 " --> pdb=" O VAL D 423 " (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 178 through 181 Processing helix chain 'M' and resid 351 through 363 removed outlier: 3.518A pdb=" N ILE M 355 " --> pdb=" O HIS M 351 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE M 356 " --> pdb=" O PRO M 352 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU M 357 " --> pdb=" O HIS M 353 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU M 362 " --> pdb=" O TYR M 358 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 398 removed outlier: 3.769A pdb=" N VAL M 368 " --> pdb=" O PRO M 364 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS M 389 " --> pdb=" O ALA M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 402 Processing helix chain 'M' and resid 409 through 415 Processing helix chain 'N' and resid 6 through 10 removed outlier: 3.550A pdb=" N LYS N 10 " --> pdb=" O ASN N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 83 No H-bonds generated for 'chain 'N' and resid 81 through 83' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.716A pdb=" N LEU N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU N 362 " --> pdb=" O TYR N 358 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 403 removed outlier: 3.606A pdb=" N VAL N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL N 386 " --> pdb=" O VAL N 382 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET N 388 " --> pdb=" O THR N 384 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS N 389 " --> pdb=" O ALA N 385 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG N 395 " --> pdb=" O CYS N 391 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.808A pdb=" N THR N 403 " --> pdb=" O PRO N 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 Processing helix chain 'O' and resid 6 through 10 removed outlier: 3.508A pdb=" N LYS O 10 " --> pdb=" O ASN O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 83 No H-bonds generated for 'chain 'O' and resid 81 through 83' Processing helix chain 'O' and resid 351 through 361 removed outlier: 3.586A pdb=" N ILE O 355 " --> pdb=" O HIS O 351 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE O 356 " --> pdb=" O PRO O 352 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU O 357 " --> pdb=" O HIS O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 398 removed outlier: 3.502A pdb=" N VAL O 368 " --> pdb=" O PRO O 364 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS O 389 " --> pdb=" O ALA O 385 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL O 390 " --> pdb=" O VAL O 386 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS O 391 " --> pdb=" O GLY O 387 " (cutoff:3.500A) Processing helix chain 'O' and resid 399 through 401 No H-bonds generated for 'chain 'O' and resid 399 through 401' Processing helix chain 'O' and resid 409 through 415 Processing helix chain 'P' and resid 6 through 10 removed outlier: 3.523A pdb=" N LYS P 10 " --> pdb=" O ASN P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'P' and resid 351 through 361 removed outlier: 3.632A pdb=" N LEU P 357 " --> pdb=" O HIS P 353 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR P 359 " --> pdb=" O ILE P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 403 removed outlier: 3.810A pdb=" N VAL P 368 " --> pdb=" O PRO P 364 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL P 369 " --> pdb=" O THR P 365 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG P 395 " --> pdb=" O CYS P 391 " (cutoff:3.500A) Proline residue: P 399 - end of helix removed outlier: 3.563A pdb=" N LEU P 402 " --> pdb=" O THR P 398 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR P 403 " --> pdb=" O PRO P 399 " (cutoff:3.500A) Processing helix chain 'P' and resid 409 through 415 Processing helix chain 'Q' and resid 146 through 151 removed outlier: 3.950A pdb=" N LYS Q 151 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 175 removed outlier: 4.944A pdb=" N SER Q 173 " --> pdb=" O HIS Q 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 152 removed outlier: 3.530A pdb=" N LYS R 151 " --> pdb=" O ASP R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 175 removed outlier: 4.989A pdb=" N SER R 173 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'S' and resid 148 through 152 removed outlier: 3.724A pdb=" N LYS S 151 " --> pdb=" O ASP S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 175 removed outlier: 3.581A pdb=" N MET S 171 " --> pdb=" O PRO S 168 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N SER S 173 " --> pdb=" O HIS S 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 148 through 152 Processing helix chain 'T' and resid 168 through 175 removed outlier: 3.597A pdb=" N MET T 171 " --> pdb=" O PRO T 168 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER T 173 " --> pdb=" O HIS T 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.879A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.957A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 92 removed outlier: 3.894A pdb=" N THR V 92 " --> pdb=" O ALA V 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.888A pdb=" N PHE U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 92 removed outlier: 3.923A pdb=" N THR X 92 " --> pdb=" O ALA X 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 83 removed outlier: 3.882A pdb=" N PHE W 83 " --> pdb=" O PRO W 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 92 removed outlier: 3.933A pdb=" N THR Z 92 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 83 removed outlier: 3.867A pdb=" N PHE Y 83 " --> pdb=" O PRO Y 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 3.854A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 132 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 48 removed outlier: 7.181A pdb=" N ALA A 121 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 120 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 177 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.586A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.586A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 79 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 106 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 77 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA9, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AB1, first strand: chain 'A' and resid 300 through 306 removed outlier: 3.654A pdb=" N SER A 300 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A 315 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 350 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.615A pdb=" N GLY A 326 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.520A pdb=" N TYR M 297 " --> pdb=" O HIS M 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.658A pdb=" N LYS B 160 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 19 removed outlier: 3.968A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS B 132 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AB7, first strand: chain 'B' and resid 42 through 48 removed outlier: 7.175A pdb=" N ALA B 121 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 177 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.545A pdb=" N TYR B 59 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.608A pdb=" N ALA B 106 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 77 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AC3, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AC4, first strand: chain 'B' and resid 300 through 306 removed outlier: 3.688A pdb=" N SER B 300 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 350 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AC6, first strand: chain 'B' and resid 387 through 388 removed outlier: 3.592A pdb=" N TYR N 297 " --> pdb=" O HIS N 307 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS N 307 " --> pdb=" O TYR N 297 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.691A pdb=" N LYS C 160 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 15 through 19 removed outlier: 4.178A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS C 132 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER C 130 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 38 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AD1, first strand: chain 'C' and resid 42 through 48 removed outlier: 7.049A pdb=" N ALA C 121 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE C 47 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 119 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 120 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 177 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.629A pdb=" N SER C 104 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 79 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 106 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 77 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD5, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD6, first strand: chain 'C' and resid 219 through 221 Processing sheet with id=AD7, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.535A pdb=" N SER C 300 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL C 315 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AD9, first strand: chain 'C' and resid 387 through 388 removed outlier: 3.656A pdb=" N TYR O 297 " --> pdb=" O HIS O 307 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS O 307 " --> pdb=" O TYR O 297 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.655A pdb=" N LYS D 160 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 15 through 19 removed outlier: 4.155A pdb=" N GLU D 30 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS D 132 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 36 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER D 130 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU D 38 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER D 128 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 15 through 19 Processing sheet with id=AE4, first strand: chain 'D' and resid 42 through 48 removed outlier: 7.109A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 120 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AE6, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.622A pdb=" N SER D 104 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 79 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 106 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AE8, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AE9, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AF1, first strand: chain 'D' and resid 296 through 306 removed outlier: 6.710A pdb=" N THR D 321 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET D 299 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS D 319 " --> pdb=" O MET D 299 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N CYS D 301 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE D 317 " --> pdb=" O CYS D 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL D 303 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL D 315 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 350 " --> pdb=" O TYR D 320 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 343 through 346 removed outlier: 3.524A pdb=" N PHE D 365 " --> pdb=" O CYS D 376 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 337 through 339 Processing sheet with id=AF4, first strand: chain 'D' and resid 387 through 388 removed outlier: 3.685A pdb=" N TYR P 297 " --> pdb=" O HIS P 307 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 17 through 19 removed outlier: 3.639A pdb=" N ALA M 17 " --> pdb=" O SER M 30 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS M 28 " --> pdb=" O CYS M 19 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 74 through 79 removed outlier: 3.585A pdb=" N THR M 74 " --> pdb=" O ASP M 71 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS M 66 " --> pdb=" O GLY M 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN M 53 " --> pdb=" O ARG M 68 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET M 70 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N SER M 51 " --> pdb=" O MET M 70 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS M 99 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N LEU M 52 " --> pdb=" O MET M 97 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N MET M 97 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ILE M 54 " --> pdb=" O GLY M 95 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N GLY M 95 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 16.920A pdb=" N ILE M 56 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 19.818A pdb=" N ILE M 93 " --> pdb=" O ILE M 56 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 84 through 86 removed outlier: 4.335A pdb=" N GLU M 109 " --> pdb=" O PHE M 129 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 149 through 156 removed outlier: 3.727A pdb=" N THR M 155 " --> pdb=" O ALA M 262 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 166 through 170 removed outlier: 4.068A pdb=" N GLY M 253 " --> pdb=" O VAL M 169 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 175 through 176 removed outlier: 3.629A pdb=" N HIS M 226 " --> pdb=" O LYS M 200 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR M 199 " --> pdb=" O GLY M 209 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY M 209 " --> pdb=" O TYR M 199 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 182 through 184 removed outlier: 3.923A pdb=" N VAL M 188 " --> pdb=" O ILE M 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS M 215 " --> pdb=" O ILE M 190 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 275 through 279 removed outlier: 3.800A pdb=" N GLN M 282 " --> pdb=" O GLY M 279 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS M 315 " --> pdb=" O LEU M 287 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.563A pdb=" N ALA N 17 " --> pdb=" O SER N 30 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 34 through 38 removed outlier: 8.887A pdb=" N LEU N 34 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER N 51 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG N 36 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN N 49 " --> pdb=" O ARG N 36 " (cutoff:3.500A) removed outlier: 10.724A pdb=" N SER N 51 " --> pdb=" O MET N 70 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET N 70 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN N 53 " --> pdb=" O ARG N 68 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYS N 66 " --> pdb=" O GLY N 55 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 34 through 38 removed outlier: 8.887A pdb=" N LEU N 34 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER N 51 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG N 36 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN N 49 " --> pdb=" O ARG N 36 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N HIS N 99 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LEU N 52 " --> pdb=" O MET N 97 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N MET N 97 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N ILE N 54 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 11.486A pdb=" N GLY N 95 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 17.070A pdb=" N ILE N 56 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 19.967A pdb=" N ILE N 93 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 84 through 86 removed outlier: 4.452A pdb=" N GLU N 109 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE N 129 " --> pdb=" O GLU N 109 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 148 through 156 Processing sheet with id=AG9, first strand: chain 'N' and resid 236 through 237 removed outlier: 4.181A pdb=" N GLY N 253 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 175 through 176 removed outlier: 4.148A pdb=" N TYR N 199 " --> pdb=" O GLY N 209 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY N 209 " --> pdb=" O TYR N 199 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 181 through 184 removed outlier: 3.580A pdb=" N ASN N 187 " --> pdb=" O GLN N 184 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL N 188 " --> pdb=" O ILE N 217 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS N 215 " --> pdb=" O ILE N 190 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 275 through 279 removed outlier: 3.700A pdb=" N GLN N 282 " --> pdb=" O GLY N 279 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS N 315 " --> pdb=" O LEU N 287 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 17 through 19 removed outlier: 3.542A pdb=" N ALA O 17 " --> pdb=" O SER O 30 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS O 28 " --> pdb=" O CYS O 19 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 34 through 38 removed outlier: 5.266A pdb=" N GLN O 49 " --> pdb=" O GLU O 35 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE O 37 " --> pdb=" O LYS O 47 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS O 47 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 10.618A pdb=" N SER O 51 " --> pdb=" O MET O 70 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET O 70 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN O 53 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS O 66 " --> pdb=" O GLY O 55 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR O 74 " --> pdb=" O ASP O 71 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 34 through 38 removed outlier: 5.266A pdb=" N GLN O 49 " --> pdb=" O GLU O 35 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE O 37 " --> pdb=" O LYS O 47 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS O 47 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA O 103 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS O 99 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N LEU O 52 " --> pdb=" O MET O 97 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N MET O 97 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N ILE O 54 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 11.527A pdb=" N GLY O 95 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 17.231A pdb=" N ILE O 56 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 20.047A pdb=" N ILE O 93 " --> pdb=" O ILE O 56 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 84 through 86 removed outlier: 4.353A pdb=" N GLU O 109 " --> pdb=" O PHE O 129 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 149 through 156 Processing sheet with id=AH9, first strand: chain 'O' and resid 236 through 237 removed outlier: 4.234A pdb=" N GLY O 253 " --> pdb=" O VAL O 169 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 175 through 176 removed outlier: 3.855A pdb=" N TYR O 199 " --> pdb=" O GLY O 209 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY O 209 " --> pdb=" O TYR O 199 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 181 through 184 removed outlier: 3.629A pdb=" N ASN O 187 " --> pdb=" O GLN O 184 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL O 188 " --> pdb=" O ILE O 217 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS O 215 " --> pdb=" O ILE O 190 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 275 through 279 removed outlier: 3.584A pdb=" N GLN O 282 " --> pdb=" O GLY O 279 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS O 315 " --> pdb=" O LEU O 287 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 17 through 19 removed outlier: 3.707A pdb=" N CYS P 28 " --> pdb=" O CYS P 19 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 74 through 79 removed outlier: 3.579A pdb=" N THR P 74 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LYS P 66 " --> pdb=" O GLY P 55 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN P 53 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET P 70 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N SER P 51 " --> pdb=" O MET P 70 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N HIS P 99 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N LEU P 52 " --> pdb=" O MET P 97 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N MET P 97 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N ILE P 54 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N GLY P 95 " --> pdb=" O ILE P 54 " (cutoff:3.500A) removed outlier: 17.066A pdb=" N ILE P 56 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 19.906A pdb=" N ILE P 93 " --> pdb=" O ILE P 56 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'P' and resid 84 through 86 removed outlier: 4.336A pdb=" N GLU P 109 " --> pdb=" O PHE P 129 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P' and resid 149 through 156 removed outlier: 3.602A pdb=" N THR P 155 " --> pdb=" O ALA P 262 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'P' and resid 236 through 237 removed outlier: 4.038A pdb=" N GLY P 253 " --> pdb=" O VAL P 169 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 175 through 176 removed outlier: 3.521A pdb=" N THR P 175 " --> pdb=" O VAL P 229 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'P' and resid 181 through 184 removed outlier: 3.907A pdb=" N VAL P 188 " --> pdb=" O ILE P 217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE P 217 " --> pdb=" O VAL P 188 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE P 190 " --> pdb=" O LYS P 215 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS P 215 " --> pdb=" O ILE P 190 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'P' and resid 197 through 200 removed outlier: 3.840A pdb=" N TYR P 199 " --> pdb=" O GLY P 209 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY P 209 " --> pdb=" O TYR P 199 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'P' and resid 275 through 279 removed outlier: 3.641A pdb=" N GLN P 282 " --> pdb=" O GLY P 279 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS P 315 " --> pdb=" O LEU P 287 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Q' and resid 143 through 144 removed outlier: 6.834A pdb=" N PHE Q 115 " --> pdb=" O TYR Q 126 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR Q 126 " --> pdb=" O PHE Q 115 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL Q 117 " --> pdb=" O MET Q 124 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR Q 126 " --> pdb=" O PRO Q 137 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU Q 162 " --> pdb=" O SER Q 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER Q 157 " --> pdb=" O LEU Q 162 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS Q 164 " --> pdb=" O LYS Q 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS Q 155 " --> pdb=" O CYS Q 164 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Q' and resid 249 through 253 removed outlier: 6.916A pdb=" N ALA Q 239 " --> pdb=" O GLY Q 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY Q 231 " --> pdb=" O ALA Q 239 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER Q 241 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TRP Q 245 " --> pdb=" O VAL Q 225 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL Q 225 " --> pdb=" O TRP Q 245 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA Q 226 " --> pdb=" O ILE Q 217 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY Q 185 " --> pdb=" O TYR Q 196 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N ALA Q 193 " --> pdb=" O PRO Q 204 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER Q 197 " --> pdb=" O ARG Q 200 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG Q 200 " --> pdb=" O SER Q 197 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE Q 201 " --> pdb=" O LEU Q 240 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU Q 240 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 143 through 144 removed outlier: 4.103A pdb=" N GLY R 125 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N HIS R 119 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL R 123 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N TYR R 126 " --> pdb=" O PRO R 137 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU R 162 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER R 157 " --> pdb=" O LEU R 162 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS R 164 " --> pdb=" O LYS R 155 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 249 through 253 removed outlier: 3.604A pdb=" N ILE R 249 " --> pdb=" O ASN R 246 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA R 239 " --> pdb=" O GLY R 231 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLY R 231 " --> pdb=" O ALA R 239 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER R 241 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP R 245 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL R 225 " --> pdb=" O TRP R 245 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE R 217 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY R 185 " --> pdb=" O TYR R 196 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA R 193 " --> pdb=" O PRO R 204 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE R 201 " --> pdb=" O LEU R 240 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 143 through 144 removed outlier: 6.929A pdb=" N PHE S 115 " --> pdb=" O TYR S 126 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR S 126 " --> pdb=" O PHE S 115 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL S 117 " --> pdb=" O MET S 124 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR S 126 " --> pdb=" O PRO S 137 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU S 162 " --> pdb=" O SER S 157 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER S 157 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS S 164 " --> pdb=" O LYS S 155 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS S 155 " --> pdb=" O CYS S 164 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'S' and resid 249 through 253 removed outlier: 3.566A pdb=" N THR S 251 " --> pdb=" O THR S 244 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER S 241 " --> pdb=" O GLY S 230 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY S 230 " --> pdb=" O SER S 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL S 243 " --> pdb=" O VAL S 228 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL S 228 " --> pdb=" O VAL S 243 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N TRP S 245 " --> pdb=" O ALA S 226 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA S 226 " --> pdb=" O TRP S 245 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE S 217 " --> pdb=" O VAL S 225 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN S 188 " --> pdb=" O PHE S 218 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY S 185 " --> pdb=" O TYR S 196 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR S 196 " --> pdb=" O GLY S 185 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ALA S 193 " --> pdb=" O PRO S 204 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE S 201 " --> pdb=" O LEU S 240 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'T' and resid 143 through 144 removed outlier: 6.666A pdb=" N PHE T 115 " --> pdb=" O TYR T 126 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR T 126 " --> pdb=" O PHE T 115 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL T 117 " --> pdb=" O MET T 124 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N TYR T 126 " --> pdb=" O PRO T 137 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU T 162 " --> pdb=" O SER T 157 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER T 157 " --> pdb=" O LEU T 162 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'T' and resid 250 through 253 removed outlier: 4.309A pdb=" N GLY T 230 " --> pdb=" O SER T 241 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL T 243 " --> pdb=" O VAL T 228 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL T 228 " --> pdb=" O VAL T 243 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N TRP T 245 " --> pdb=" O ALA T 226 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ALA T 226 " --> pdb=" O TRP T 245 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE T 217 " --> pdb=" O VAL T 225 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE T 218 " --> pdb=" O ASN T 188 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN T 188 " --> pdb=" O PHE T 218 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ALA T 193 " --> pdb=" O PRO T 204 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE T 201 " --> pdb=" O LEU T 240 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE T 203 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.846A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.328A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AK6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AK7, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.617A pdb=" N TYR H 60 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP H 36 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA H 100 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER H 117 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.617A pdb=" N TYR H 60 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP H 36 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA H 100 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR H 122 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'V' and resid 3 through 7 Processing sheet with id=AL1, first strand: chain 'V' and resid 11 through 12 Processing sheet with id=AL2, first strand: chain 'V' and resid 59 through 61 removed outlier: 3.502A pdb=" N TYR V 60 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP V 38 " --> pdb=" O ILE V 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR V 52 " --> pdb=" O TRP V 36 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP V 36 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA V 100 " --> pdb=" O TYR V 35 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER V 117 " --> pdb=" O ARG V 99 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'V' and resid 59 through 61 removed outlier: 3.502A pdb=" N TYR V 60 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP V 38 " --> pdb=" O ILE V 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR V 52 " --> pdb=" O TRP V 36 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP V 36 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA V 100 " --> pdb=" O TYR V 35 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR V 122 " --> pdb=" O TYR V 95 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'U' and resid 4 through 7 removed outlier: 3.834A pdb=" N VAL U 19 " --> pdb=" O ILE U 75 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP U 70 " --> pdb=" O SER U 67 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.326A pdb=" N VAL U 11 " --> pdb=" O GLU U 105 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU U 33 " --> pdb=" O TYR U 49 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR U 49 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'X' and resid 3 through 7 removed outlier: 3.605A pdb=" N PHE X 80 " --> pdb=" O CYS X 22 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'X' and resid 11 through 12 Processing sheet with id=AL8, first strand: chain 'X' and resid 59 through 61 removed outlier: 3.672A pdb=" N TYR X 60 " --> pdb=" O TYR X 52 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP X 38 " --> pdb=" O ILE X 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR X 52 " --> pdb=" O TRP X 36 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP X 36 " --> pdb=" O TYR X 52 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA X 100 " --> pdb=" O TYR X 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER X 117 " --> pdb=" O ARG X 99 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'X' and resid 59 through 61 removed outlier: 3.672A pdb=" N TYR X 60 " --> pdb=" O TYR X 52 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP X 38 " --> pdb=" O ILE X 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR X 52 " --> pdb=" O TRP X 36 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP X 36 " --> pdb=" O TYR X 52 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA X 100 " --> pdb=" O TYR X 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR X 122 " --> pdb=" O TYR X 95 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'W' and resid 4 through 7 removed outlier: 3.827A pdb=" N VAL W 19 " --> pdb=" O ILE W 75 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP W 70 " --> pdb=" O SER W 67 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'W' and resid 10 through 13 removed outlier: 7.277A pdb=" N LEU W 33 " --> pdb=" O TYR W 49 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR W 49 " --> pdb=" O LEU W 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP W 35 " --> pdb=" O LEU W 47 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'Z' and resid 3 through 7 removed outlier: 3.636A pdb=" N PHE Z 80 " --> pdb=" O CYS Z 22 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER Z 81 " --> pdb=" O SER Z 72 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'Z' and resid 11 through 12 Processing sheet with id=AM5, first strand: chain 'Z' and resid 59 through 61 removed outlier: 3.699A pdb=" N TYR Z 60 " --> pdb=" O TYR Z 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR Z 52 " --> pdb=" O TYR Z 60 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP Z 38 " --> pdb=" O ILE Z 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR Z 52 " --> pdb=" O TRP Z 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP Z 36 " --> pdb=" O TYR Z 52 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA Z 100 " --> pdb=" O TYR Z 35 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER Z 117 " --> pdb=" O ARG Z 99 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'Z' and resid 59 through 61 removed outlier: 3.699A pdb=" N TYR Z 60 " --> pdb=" O TYR Z 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR Z 52 " --> pdb=" O TYR Z 60 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP Z 38 " --> pdb=" O ILE Z 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR Z 52 " --> pdb=" O TRP Z 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP Z 36 " --> pdb=" O TYR Z 52 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA Z 100 " --> pdb=" O TYR Z 35 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR Z 122 " --> pdb=" O TYR Z 95 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.792A pdb=" N VAL Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP Y 70 " --> pdb=" O SER Y 67 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'Y' and resid 10 through 13 removed outlier: 3.535A pdb=" N ALA Y 13 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU Y 33 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR Y 49 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) 1407 hydrogen bonds defined for protein. 3606 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: 18.66 Time building geometry restraints manager: 14.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 12383 1.35 - 1.47: 10043 1.47 - 1.60: 16422 1.60 - 1.73: 0 1.73 - 1.85: 348 Bond restraints: 39196 Sorted by residual: bond pdb=" CB PRO R 255 " pdb=" CG PRO R 255 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.33e+00 bond pdb=" CB CYS B 94 " pdb=" SG CYS B 94 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.29e+00 bond pdb=" CB PRO Q 204 " pdb=" CG PRO Q 204 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.26e+00 bond pdb=" CB CYS B 62 " pdb=" SG CYS B 62 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.13e+00 bond pdb=" C1 NAG N 501 " pdb=" O5 NAG N 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.33e+00 ... (remaining 39191 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.35: 854 104.35 - 111.79: 19091 111.79 - 119.23: 12874 119.23 - 126.67: 19890 126.67 - 134.11: 695 Bond angle restraints: 53404 Sorted by residual: angle pdb=" CA CYS M 153 " pdb=" CB CYS M 153 " pdb=" SG CYS M 153 " ideal model delta sigma weight residual 114.40 124.85 -10.45 2.30e+00 1.89e-01 2.07e+01 angle pdb=" CA CYS P 153 " pdb=" CB CYS P 153 " pdb=" SG CYS P 153 " ideal model delta sigma weight residual 114.40 124.67 -10.27 2.30e+00 1.89e-01 1.99e+01 angle pdb=" CA CYS A 63 " pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " ideal model delta sigma weight residual 114.40 124.32 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" CA PRO Q 204 " pdb=" N PRO Q 204 " pdb=" CD PRO Q 204 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" CA ASP D 97 " pdb=" CB ASP D 97 " pdb=" CG ASP D 97 " ideal model delta sigma weight residual 112.60 116.71 -4.11 1.00e+00 1.00e+00 1.69e+01 ... (remaining 53399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 21805 18.04 - 36.09: 1400 36.09 - 54.13: 369 54.13 - 72.18: 73 72.18 - 90.22: 33 Dihedral angle restraints: 23680 sinusoidal: 9352 harmonic: 14328 Sorted by residual: dihedral pdb=" CB CYS N 153 " pdb=" SG CYS N 153 " pdb=" SG CYS N 266 " pdb=" CB CYS N 266 " ideal model delta sinusoidal sigma weight residual -86.00 -173.04 87.04 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS B 62 " pdb=" SG CYS B 62 " pdb=" SG CYS B 94 " pdb=" CB CYS B 94 " ideal model delta sinusoidal sigma weight residual -86.00 -141.48 55.48 1 1.00e+01 1.00e-02 4.16e+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 93.00 148.23 -55.23 1 1.00e+01 1.00e-02 4.12e+01 ... (remaining 23677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5276 0.072 - 0.144: 731 0.144 - 0.215: 21 0.215 - 0.287: 3 0.287 - 0.359: 5 Chirality restraints: 6036 Sorted by residual: 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 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+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 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C1 NAG N 501 " pdb=" ND2 ASN N 263 " pdb=" C2 NAG N 501 " pdb=" O5 NAG N 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 6033 not shown) Planarity restraints: 6860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS S 136 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO S 137 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO S 137 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO S 137 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Q 203 " -0.085 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO Q 204 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO Q 204 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO Q 204 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL O 321 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO O 322 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO O 322 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO O 322 " -0.059 5.00e-02 4.00e+02 ... (remaining 6857 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 514 2.67 - 3.23: 31748 3.23 - 3.79: 50884 3.79 - 4.34: 64764 4.34 - 4.90: 114690 Nonbonded interactions: 262600 Sorted by model distance: nonbonded pdb=" OD1 ASP O 117 " pdb=" N SER O 118 " model vdw 2.116 2.520 nonbonded pdb=" OD1 ASP M 117 " pdb=" N SER M 118 " model vdw 2.163 2.520 nonbonded pdb=" OG SER A 57 " pdb=" O VAL M 242 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR A 10 " pdb=" OH TYR A 15 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR N 69 " pdb=" OD1 ASP N 117 " model vdw 2.213 2.440 ... (remaining 262595 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: 2.060 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: 0.040 Extract box with map and model: 10.840 Check model and map are aligned: 0.530 Set scattering table: 0.360 Process input model: 98.250 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 0.091 39196 Z= 0.200 Angle : 0.618 12.921 53404 Z= 0.328 Chirality : 0.047 0.359 6036 Planarity : 0.007 0.131 6848 Dihedral : 13.244 90.223 14296 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.10 % Allowed : 11.53 % Favored : 88.38 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.19 % 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: -0.27 (0.11), residues: 4916 helix: 1.48 (0.24), residues: 409 sheet: 0.25 (0.12), residues: 1734 loop : -0.70 (0.10), residues: 2773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 189 HIS 0.008 0.001 HIS Q 170 PHE 0.027 0.002 PHE B 95 TYR 0.020 0.001 TYR D 59 ARG 0.005 0.001 ARG B 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 716 time to evaluate : 4.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 28 CYS cc_start: 0.7127 (p) cc_final: 0.6655 (p) REVERT: O 24 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7138 (mm-30) REVERT: P 24 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7171 (mm-30) REVERT: P 200 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8162 (ttmm) REVERT: P 223 ASP cc_start: 0.7334 (t0) cc_final: 0.6950 (t0) REVERT: Q 132 ASP cc_start: 0.6823 (p0) cc_final: 0.6516 (p0) REVERT: S 172 LYS cc_start: 0.7813 (tttt) cc_final: 0.7570 (tttt) outliers start: 4 outliers final: 2 residues processed: 719 average time/residue: 0.5362 time to fit residues: 613.4087 Evaluate side-chains 677 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 675 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain O residue 192 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 408 optimal weight: 40.0000 chunk 366 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 247 optimal weight: 0.0670 chunk 195 optimal weight: 0.0980 chunk 379 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 230 optimal weight: 6.9990 chunk 282 optimal weight: 0.1980 chunk 439 optimal weight: 9.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 186 ASN A 222 GLN A 389 ASN C 252 GLN M 127 HIS M 158 GLN M 184 GLN M 234 ASN M 273 ASN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN N 53 GLN N 158 GLN N 184 GLN N 226 HIS N 234 ASN N 273 ASN O 53 GLN O 183 GLN O 193 ASN P 183 GLN P 184 GLN P 193 ASN P 273 ASN P 299 ASN P 302 GLN ** Q 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS R 139 HIS S 220 ASN T 190 HIS L 92 ASN H 109 ASN V 109 ASN X 109 ASN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 39196 Z= 0.161 Angle : 0.566 9.316 53404 Z= 0.311 Chirality : 0.046 0.272 6036 Planarity : 0.005 0.082 6848 Dihedral : 5.276 53.106 5606 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.81 % Allowed : 11.31 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.12 (0.11), residues: 4916 helix: 1.57 (0.24), residues: 462 sheet: 0.40 (0.12), residues: 1756 loop : -0.69 (0.11), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 330 HIS 0.009 0.001 HIS Q 170 PHE 0.013 0.001 PHE R 201 TYR 0.011 0.001 TYR W 86 ARG 0.007 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 662 time to evaluate : 3.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 ARG cc_start: 0.7688 (mtp85) cc_final: 0.7343 (ttm-80) REVERT: C 158 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: D 343 ASP cc_start: 0.7427 (p0) cc_final: 0.7033 (p0) REVERT: M 19 CYS cc_start: 0.7902 (t) cc_final: 0.7548 (t) REVERT: M 180 LEU cc_start: 0.7590 (mt) cc_final: 0.7250 (mt) REVERT: M 324 GLU cc_start: 0.7818 (mp0) cc_final: 0.7381 (mp0) REVERT: N 188 VAL cc_start: 0.8088 (m) cc_final: 0.7824 (m) REVERT: N 344 THR cc_start: 0.8633 (t) cc_final: 0.8376 (p) REVERT: N 357 LEU cc_start: 0.8254 (tp) cc_final: 0.8022 (tp) REVERT: N 375 SER cc_start: 0.8338 (t) cc_final: 0.8027 (m) REVERT: N 379 LEU cc_start: 0.8199 (mm) cc_final: 0.7977 (mt) REVERT: N 382 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8323 (p) REVERT: O 24 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7133 (mm-30) REVERT: O 181 MET cc_start: 0.8378 (mtm) cc_final: 0.8177 (mtt) REVERT: O 366 MET cc_start: 0.7091 (mpp) cc_final: 0.6781 (mpp) REVERT: O 382 VAL cc_start: 0.8684 (t) cc_final: 0.8429 (p) REVERT: O 394 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8364 (ttm-80) REVERT: P 102 LEU cc_start: 0.8667 (tt) cc_final: 0.8353 (tp) REVERT: P 200 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8131 (ttmm) REVERT: P 223 ASP cc_start: 0.7220 (t0) cc_final: 0.6814 (t0) REVERT: Q 132 ASP cc_start: 0.6853 (p0) cc_final: 0.6572 (p0) REVERT: T 171 MET cc_start: 0.8499 (mtp) cc_final: 0.8242 (mtp) outliers start: 76 outliers final: 42 residues processed: 697 average time/residue: 0.5604 time to fit residues: 628.7377 Evaluate side-chains 679 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 635 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 181 MET Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 380 SER Chi-restraints excluded: chain O residue 381 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 244 optimal weight: 5.9990 chunk 136 optimal weight: 0.0870 chunk 365 optimal weight: 0.3980 chunk 299 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 440 optimal weight: 8.9990 chunk 475 optimal weight: 40.0000 chunk 392 optimal weight: 0.2980 chunk 436 optimal weight: 50.0000 chunk 150 optimal weight: 0.8980 chunk 353 optimal weight: 0.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 152 HIS ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN O 53 GLN O 184 GLN P 193 ASN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 39196 Z= 0.136 Angle : 0.508 8.478 53404 Z= 0.271 Chirality : 0.044 0.320 6036 Planarity : 0.005 0.066 6848 Dihedral : 4.907 52.474 5605 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.81 % Allowed : 12.81 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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 (0.12), residues: 4916 helix: 1.58 (0.25), residues: 460 sheet: 0.37 (0.12), residues: 1845 loop : -0.73 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 49 HIS 0.049 0.001 HIS R 139 PHE 0.017 0.001 PHE C 436 TYR 0.015 0.001 TYR C 320 ARG 0.007 0.000 ARG M 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 670 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.8159 (mtm) cc_final: 0.7909 (mtm) REVERT: B 155 THR cc_start: 0.8195 (p) cc_final: 0.7919 (m) REVERT: C 123 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7368 (ttm-80) REVERT: C 160 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7776 (mtmt) REVERT: C 373 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7995 (mm-40) REVERT: D 10 THR cc_start: 0.8131 (m) cc_final: 0.7875 (m) REVERT: D 343 ASP cc_start: 0.7463 (p0) cc_final: 0.7085 (p0) REVERT: M 180 LEU cc_start: 0.7631 (mt) cc_final: 0.7420 (mp) REVERT: M 394 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: N 188 VAL cc_start: 0.8084 (m) cc_final: 0.7837 (m) REVERT: N 291 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6818 (p-80) REVERT: N 357 LEU cc_start: 0.8227 (tp) cc_final: 0.7982 (tp) REVERT: N 375 SER cc_start: 0.8192 (t) cc_final: 0.7972 (m) REVERT: N 382 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7980 (p) REVERT: O 24 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7032 (mm-30) REVERT: O 195 GLN cc_start: 0.7895 (mt0) cc_final: 0.7546 (mt0) REVERT: O 373 VAL cc_start: 0.8653 (t) cc_final: 0.8320 (m) REVERT: O 394 ARG cc_start: 0.8452 (ttm110) cc_final: 0.8215 (ttm170) REVERT: P 200 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8058 (tttt) REVERT: P 223 ASP cc_start: 0.7144 (t0) cc_final: 0.6761 (t0) REVERT: Q 132 ASP cc_start: 0.6857 (p0) cc_final: 0.6628 (p0) REVERT: Q 156 ARG cc_start: 0.8112 (ptm-80) cc_final: 0.7750 (ptm-80) REVERT: Q 171 MET cc_start: 0.8015 (mpp) cc_final: 0.7768 (mmt) REVERT: R 172 LYS cc_start: 0.8423 (mtmm) cc_final: 0.7952 (mttp) REVERT: T 171 MET cc_start: 0.8445 (mtp) cc_final: 0.8205 (mtp) outliers start: 76 outliers final: 49 residues processed: 705 average time/residue: 0.5224 time to fit residues: 592.0546 Evaluate side-chains 687 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 636 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 181 MET Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 198 ARG Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 164 CYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain W residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 435 optimal weight: 50.0000 chunk 331 optimal weight: 0.8980 chunk 228 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 441 optimal weight: 0.0060 chunk 467 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 418 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 439 HIS D 230 HIS ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN N 226 HIS O 131 HIS P 131 HIS P 193 ASN R 139 HIS L 79 GLN X 79 GLN Z 1 GLN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 39196 Z= 0.250 Angle : 0.584 10.990 53404 Z= 0.318 Chirality : 0.046 0.450 6036 Planarity : 0.006 0.061 6848 Dihedral : 5.213 53.947 5605 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.73 % Allowed : 13.59 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 4916 helix: 1.43 (0.25), residues: 460 sheet: 0.34 (0.12), residues: 1772 loop : -1.03 (0.11), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 49 HIS 0.010 0.002 HIS P 99 PHE 0.025 0.002 PHE C 436 TYR 0.017 0.002 TYR D 122 ARG 0.007 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 657 time to evaluate : 4.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7951 (mtp-110) REVERT: B 155 THR cc_start: 0.8248 (p) cc_final: 0.8014 (m) REVERT: C 43 SER cc_start: 0.7843 (p) cc_final: 0.7609 (m) REVERT: C 45 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7886 (t0) REVERT: C 123 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7450 (ttm-80) REVERT: C 210 SER cc_start: 0.8427 (m) cc_final: 0.8169 (m) REVERT: D 130 SER cc_start: 0.8830 (p) cc_final: 0.8364 (m) REVERT: M 223 ASP cc_start: 0.7148 (t0) cc_final: 0.6668 (t0) REVERT: M 394 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7598 (ttm-80) REVERT: N 24 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7216 (mp0) REVERT: N 43 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7278 (p0) REVERT: N 188 VAL cc_start: 0.8078 (m) cc_final: 0.7808 (m) REVERT: N 357 LEU cc_start: 0.8208 (tp) cc_final: 0.7993 (tp) REVERT: N 382 VAL cc_start: 0.8454 (p) cc_final: 0.8190 (p) REVERT: O 24 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7256 (mm-30) REVERT: O 87 THR cc_start: 0.7742 (p) cc_final: 0.7216 (t) REVERT: O 195 GLN cc_start: 0.8002 (mt0) cc_final: 0.7682 (mt0) REVERT: O 223 ASP cc_start: 0.7926 (t0) cc_final: 0.7579 (t0) REVERT: O 373 VAL cc_start: 0.8625 (t) cc_final: 0.8320 (m) REVERT: O 382 VAL cc_start: 0.8570 (t) cc_final: 0.8333 (p) REVERT: O 394 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8248 (ttm170) REVERT: P 52 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7623 (pp) REVERT: P 70 MET cc_start: 0.8254 (tpp) cc_final: 0.7661 (tpp) REVERT: P 200 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8077 (tttt) REVERT: P 223 ASP cc_start: 0.7214 (t0) cc_final: 0.6871 (t0) REVERT: Q 156 ARG cc_start: 0.8151 (ptm-80) cc_final: 0.7823 (ptm-80) REVERT: Q 171 MET cc_start: 0.8023 (mpp) cc_final: 0.7791 (mmt) REVERT: R 172 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7772 (mttp) REVERT: S 172 LYS cc_start: 0.7753 (tttt) cc_final: 0.7531 (tmtt) REVERT: T 171 MET cc_start: 0.8452 (mtp) cc_final: 0.8211 (mtp) outliers start: 115 outliers final: 82 residues processed: 725 average time/residue: 0.5132 time to fit residues: 599.5402 Evaluate side-chains 725 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 639 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 5 THR 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 202 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 390 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 153 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 182 THR Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 379 LEU Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 382 VAL Chi-restraints excluded: chain P residue 391 CYS Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 164 CYS Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 228 VAL Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 389 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 348 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 399 optimal weight: 20.0000 chunk 323 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 238 optimal weight: 0.0030 chunk 419 optimal weight: 0.1980 chunk 118 optimal weight: 6.9990 overall best weight: 2.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 252 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 ASN R 139 HIS R 170 HIS S 190 HIS ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 39196 Z= 0.315 Angle : 0.615 11.003 53404 Z= 0.334 Chirality : 0.048 0.484 6036 Planarity : 0.006 0.061 6848 Dihedral : 5.454 59.484 5605 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.16 % Allowed : 13.95 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.76 (0.11), residues: 4916 helix: 1.20 (0.25), residues: 462 sheet: 0.15 (0.12), residues: 1781 loop : -1.29 (0.11), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 330 HIS 0.035 0.002 HIS R 139 PHE 0.029 0.002 PHE R 201 TYR 0.020 0.002 TYR B 51 ARG 0.008 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 676 time to evaluate : 4.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.8040 (mtp-110) REVERT: B 155 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8052 (m) REVERT: B 211 LYS cc_start: 0.8098 (mttt) cc_final: 0.7866 (mttt) REVERT: C 43 SER cc_start: 0.8009 (p) cc_final: 0.7739 (m) REVERT: C 123 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7525 (ttm-80) REVERT: C 210 SER cc_start: 0.8436 (m) cc_final: 0.8177 (m) REVERT: C 362 SER cc_start: 0.8597 (t) cc_final: 0.8372 (p) REVERT: C 373 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8120 (mm-40) REVERT: D 130 SER cc_start: 0.8824 (p) cc_final: 0.8390 (m) REVERT: D 188 ASP cc_start: 0.8052 (t0) cc_final: 0.7800 (t0) REVERT: M 223 ASP cc_start: 0.7164 (t0) cc_final: 0.6701 (t0) REVERT: M 394 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7623 (ttm-80) REVERT: N 24 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7372 (mp0) REVERT: N 43 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7409 (p0) REVERT: N 188 VAL cc_start: 0.7883 (m) cc_final: 0.7623 (m) REVERT: N 357 LEU cc_start: 0.8208 (tp) cc_final: 0.8002 (tp) REVERT: N 382 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8222 (p) REVERT: O 24 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7380 (mm-30) REVERT: O 64 TRP cc_start: 0.6945 (p-90) cc_final: 0.6351 (p-90) REVERT: O 87 THR cc_start: 0.7809 (p) cc_final: 0.7259 (t) REVERT: O 179 THR cc_start: 0.8675 (m) cc_final: 0.8327 (p) REVERT: O 195 GLN cc_start: 0.8011 (mt0) cc_final: 0.7711 (mt0) REVERT: O 223 ASP cc_start: 0.7959 (t0) cc_final: 0.7670 (t0) REVERT: O 382 VAL cc_start: 0.8567 (t) cc_final: 0.8358 (p) REVERT: O 394 ARG cc_start: 0.8489 (ttm110) cc_final: 0.8181 (ttm-80) REVERT: P 52 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7656 (pp) REVERT: P 70 MET cc_start: 0.8258 (tpp) cc_final: 0.7681 (tpp) REVERT: P 158 GLN cc_start: 0.8374 (mt0) cc_final: 0.8127 (mt0) REVERT: P 200 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8090 (tttt) REVERT: P 223 ASP cc_start: 0.7214 (t0) cc_final: 0.6904 (t0) REVERT: P 305 ASN cc_start: 0.8064 (m-40) cc_final: 0.7751 (t0) REVERT: Q 156 ARG cc_start: 0.8140 (ptm-80) cc_final: 0.7831 (ptm-80) REVERT: Q 171 MET cc_start: 0.8042 (mpp) cc_final: 0.7835 (mmt) REVERT: R 172 LYS cc_start: 0.8444 (mtmm) cc_final: 0.7885 (mttp) REVERT: S 172 LYS cc_start: 0.7759 (tttt) cc_final: 0.7537 (tmtt) REVERT: T 135 MET cc_start: 0.8643 (mtp) cc_final: 0.8416 (mtm) outliers start: 133 outliers final: 99 residues processed: 745 average time/residue: 0.5136 time to fit residues: 620.3753 Evaluate side-chains 756 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 652 time to evaluate : 4.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 5 THR 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 133 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 390 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 153 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 182 THR Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 379 LEU Chi-restraints excluded: chain O residue 381 MET Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 36 ARG Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 391 CYS Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 164 CYS Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 228 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 157 optimal weight: 2.9990 chunk 421 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 468 optimal weight: 9.9990 chunk 388 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 ASN R 139 HIS S 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 39196 Z= 0.361 Angle : 0.648 9.802 53404 Z= 0.353 Chirality : 0.049 0.461 6036 Planarity : 0.007 0.068 6848 Dihedral : 5.653 59.690 5605 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.52 % Allowed : 14.04 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.96 (0.11), residues: 4916 helix: 1.03 (0.25), residues: 462 sheet: 0.24 (0.13), residues: 1611 loop : -1.52 (0.10), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 189 HIS 0.037 0.002 HIS R 139 PHE 0.035 0.002 PHE R 201 TYR 0.023 0.002 TYR B 51 ARG 0.009 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 675 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8091 (mtp-110) REVERT: A 405 THR cc_start: 0.7133 (m) cc_final: 0.5603 (t) REVERT: B 167 SER cc_start: 0.8725 (p) cc_final: 0.8365 (t) REVERT: B 211 LYS cc_start: 0.8120 (mttt) cc_final: 0.7893 (mttt) REVERT: C 43 SER cc_start: 0.8099 (p) cc_final: 0.7802 (m) REVERT: C 210 SER cc_start: 0.8449 (m) cc_final: 0.8233 (m) REVERT: C 299 MET cc_start: 0.8510 (mtp) cc_final: 0.8274 (mtp) REVERT: D 130 SER cc_start: 0.8814 (p) cc_final: 0.8407 (m) REVERT: D 188 ASP cc_start: 0.8092 (t0) cc_final: 0.7832 (t0) REVERT: M 223 ASP cc_start: 0.7200 (t0) cc_final: 0.6731 (t0) REVERT: M 265 THR cc_start: 0.8679 (p) cc_final: 0.8476 (m) REVERT: M 394 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: N 24 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7495 (mp0) REVERT: N 149 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7430 (ttpp) REVERT: N 188 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7602 (m) REVERT: N 344 THR cc_start: 0.8642 (t) cc_final: 0.8278 (p) REVERT: O 24 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7467 (mm-30) REVERT: O 64 TRP cc_start: 0.6959 (p-90) cc_final: 0.6357 (p-90) REVERT: O 87 THR cc_start: 0.7844 (p) cc_final: 0.7303 (t) REVERT: O 179 THR cc_start: 0.8688 (m) cc_final: 0.8356 (p) REVERT: O 195 GLN cc_start: 0.8047 (mt0) cc_final: 0.7763 (mt0) REVERT: O 223 ASP cc_start: 0.8034 (t0) cc_final: 0.7721 (t0) REVERT: O 382 VAL cc_start: 0.8573 (t) cc_final: 0.8350 (p) REVERT: O 393 ARG cc_start: 0.8104 (ttt90) cc_final: 0.7565 (ttt180) REVERT: O 394 ARG cc_start: 0.8501 (ttm110) cc_final: 0.8217 (ttm-80) REVERT: P 52 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7645 (pp) REVERT: P 70 MET cc_start: 0.8259 (tpp) cc_final: 0.7712 (tpp) REVERT: P 181 MET cc_start: 0.7695 (mtt) cc_final: 0.7456 (mtt) REVERT: P 200 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7888 (ttmm) REVERT: P 223 ASP cc_start: 0.7259 (t0) cc_final: 0.7023 (t0) REVERT: P 265 THR cc_start: 0.8659 (p) cc_final: 0.8399 (m) REVERT: P 305 ASN cc_start: 0.8087 (m-40) cc_final: 0.7778 (t0) REVERT: P 401 GLU cc_start: 0.7473 (tp30) cc_final: 0.7142 (tp30) REVERT: R 172 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8203 (mtmm) REVERT: R 178 PHE cc_start: 0.8215 (p90) cc_final: 0.7993 (p90) REVERT: S 172 LYS cc_start: 0.7828 (tttt) cc_final: 0.7579 (tmtt) outliers start: 148 outliers final: 125 residues processed: 750 average time/residue: 0.5294 time to fit residues: 640.1352 Evaluate side-chains 790 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 661 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR 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 94 CYS Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 356 ILE Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain M residue 384 THR Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 153 CYS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 390 VAL Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 153 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 182 THR Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 379 LEU Chi-restraints excluded: chain O residue 381 MET Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 36 ARG Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 199 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 382 VAL Chi-restraints excluded: chain P residue 391 CYS Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 164 CYS Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 251 THR Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 220 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 228 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 451 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 266 optimal weight: 0.6980 chunk 341 optimal weight: 2.9990 chunk 264 optimal weight: 0.0020 chunk 394 optimal weight: 0.2980 chunk 261 optimal weight: 4.9990 chunk 466 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 ASN Q 111 ASN R 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39196 Z= 0.137 Angle : 0.521 12.224 53404 Z= 0.274 Chirality : 0.044 0.380 6036 Planarity : 0.005 0.056 6848 Dihedral : 5.141 59.846 5605 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 15.73 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.70 (0.12), residues: 4916 helix: 1.46 (0.26), residues: 460 sheet: 0.26 (0.12), residues: 1763 loop : -1.35 (0.11), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 49 HIS 0.036 0.001 HIS R 139 PHE 0.025 0.001 PHE C 436 TYR 0.009 0.001 TYR C 15 ARG 0.007 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 666 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.8435 (mtm) cc_final: 0.8191 (mtt) REVERT: A 212 ASP cc_start: 0.7276 (m-30) cc_final: 0.6747 (p0) REVERT: A 366 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7884 (mtp-110) REVERT: A 370 CYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6813 (m) REVERT: B 211 LYS cc_start: 0.8199 (mttt) cc_final: 0.7959 (mttt) REVERT: C 210 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8148 (m) REVERT: D 45 ASP cc_start: 0.7955 (t0) cc_final: 0.7503 (t0) REVERT: D 130 SER cc_start: 0.8799 (p) cc_final: 0.8363 (m) REVERT: M 223 ASP cc_start: 0.7033 (t0) cc_final: 0.6607 (t0) REVERT: M 225 CYS cc_start: 0.6507 (m) cc_final: 0.6166 (m) REVERT: N 24 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7396 (mp0) REVERT: N 188 VAL cc_start: 0.8086 (m) cc_final: 0.7806 (m) REVERT: O 24 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7320 (mm-30) REVERT: O 64 TRP cc_start: 0.6888 (p-90) cc_final: 0.6295 (p-90) REVERT: O 179 THR cc_start: 0.8685 (m) cc_final: 0.8371 (p) REVERT: O 195 GLN cc_start: 0.7922 (mt0) cc_final: 0.7582 (mt0) REVERT: O 223 ASP cc_start: 0.7942 (t0) cc_final: 0.7654 (t0) REVERT: O 366 MET cc_start: 0.6375 (mpp) cc_final: 0.6105 (mpp) REVERT: O 373 VAL cc_start: 0.8460 (t) cc_final: 0.8127 (m) REVERT: O 382 VAL cc_start: 0.8497 (t) cc_final: 0.8265 (p) REVERT: O 393 ARG cc_start: 0.8123 (ttt90) cc_final: 0.7532 (ttt180) REVERT: P 70 MET cc_start: 0.8131 (tpp) cc_final: 0.7622 (tpp) REVERT: P 181 MET cc_start: 0.7700 (mtt) cc_final: 0.7413 (mtt) REVERT: P 200 LYS cc_start: 0.8333 (ttmt) cc_final: 0.8051 (tttt) REVERT: P 223 ASP cc_start: 0.7092 (t0) cc_final: 0.6814 (t0) REVERT: P 265 THR cc_start: 0.8627 (p) cc_final: 0.8408 (m) REVERT: P 305 ASN cc_start: 0.7869 (m-40) cc_final: 0.7600 (t0) REVERT: R 172 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7806 (mttp) REVERT: S 172 LYS cc_start: 0.7766 (tttt) cc_final: 0.7507 (tmtt) outliers start: 96 outliers final: 71 residues processed: 716 average time/residue: 0.5375 time to fit residues: 625.0135 Evaluate side-chains 723 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 649 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 313 HIS Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 153 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 347 THR Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain Q residue 111 ASN Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 251 THR Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 288 optimal weight: 0.0270 chunk 186 optimal weight: 0.8980 chunk 278 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 317 optimal weight: 0.5980 chunk 230 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN M 307 HIS ** N 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 341 GLN P 187 ASN P 193 ASN Q 111 ASN R 139 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39196 Z= 0.139 Angle : 0.519 11.334 53404 Z= 0.270 Chirality : 0.044 0.336 6036 Planarity : 0.005 0.054 6848 Dihedral : 5.003 59.867 5605 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.19 % Allowed : 15.97 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.59 (0.12), residues: 4916 helix: 1.59 (0.26), residues: 460 sheet: 0.32 (0.12), residues: 1824 loop : -1.31 (0.11), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 49 HIS 0.026 0.001 HIS R 139 PHE 0.028 0.001 PHE C 436 TYR 0.011 0.001 TYR S 160 ARG 0.008 0.000 ARG S 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 656 time to evaluate : 4.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.7284 (m-30) cc_final: 0.6749 (p0) REVERT: A 366 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7862 (mtp-110) REVERT: A 370 CYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6786 (m) REVERT: B 211 LYS cc_start: 0.8172 (mttt) cc_final: 0.7969 (mttt) REVERT: C 210 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.8146 (m) REVERT: M 223 ASP cc_start: 0.7039 (t0) cc_final: 0.6644 (t0) REVERT: M 225 CYS cc_start: 0.6396 (m) cc_final: 0.5985 (m) REVERT: N 24 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7377 (mp0) REVERT: N 149 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7292 (ttpp) REVERT: N 188 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7775 (m) REVERT: O 24 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7347 (mm-30) REVERT: O 64 TRP cc_start: 0.6892 (p-90) cc_final: 0.6281 (p-90) REVERT: O 179 THR cc_start: 0.8703 (m) cc_final: 0.8374 (p) REVERT: O 195 GLN cc_start: 0.7916 (mt0) cc_final: 0.7590 (mt0) REVERT: O 223 ASP cc_start: 0.7933 (t0) cc_final: 0.7700 (t0) REVERT: O 373 VAL cc_start: 0.8365 (t) cc_final: 0.8045 (m) REVERT: O 393 ARG cc_start: 0.8125 (ttt90) cc_final: 0.7538 (ttt180) REVERT: P 70 MET cc_start: 0.8143 (tpp) cc_final: 0.7614 (tpp) REVERT: P 181 MET cc_start: 0.7683 (mtt) cc_final: 0.7447 (mtt) REVERT: P 200 LYS cc_start: 0.8328 (ttmt) cc_final: 0.8046 (tttt) REVERT: P 223 ASP cc_start: 0.7098 (t0) cc_final: 0.6813 (t0) REVERT: P 265 THR cc_start: 0.8629 (p) cc_final: 0.8417 (m) REVERT: R 172 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7706 (mttp) REVERT: S 172 LYS cc_start: 0.7780 (tttt) cc_final: 0.7488 (tmtt) REVERT: T 135 MET cc_start: 0.8664 (mtp) cc_final: 0.8445 (mtp) outliers start: 92 outliers final: 72 residues processed: 709 average time/residue: 0.5344 time to fit residues: 608.2155 Evaluate side-chains 725 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 648 time to evaluate : 4.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 153 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 347 THR Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 164 CYS Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 251 THR Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 424 optimal weight: 10.0000 chunk 446 optimal weight: 10.0000 chunk 407 optimal weight: 0.6980 chunk 434 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 392 optimal weight: 0.9990 chunk 411 optimal weight: 4.9990 chunk 433 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 353 GLN ** N 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 127 HIS P 193 ASN R 139 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 39196 Z= 0.317 Angle : 0.626 11.132 53404 Z= 0.335 Chirality : 0.048 0.397 6036 Planarity : 0.006 0.058 6848 Dihedral : 5.394 59.435 5605 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.66 % Allowed : 15.61 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.91 (0.11), residues: 4916 helix: 1.28 (0.25), residues: 462 sheet: 0.27 (0.13), residues: 1702 loop : -1.58 (0.11), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 339 HIS 0.020 0.002 HIS R 139 PHE 0.035 0.002 PHE C 436 TYR 0.022 0.002 TYR S 160 ARG 0.009 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 654 time to evaluate : 4.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.7366 (m-30) cc_final: 0.6872 (p0) REVERT: A 366 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8028 (mtp-110) REVERT: A 370 CYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6864 (m) REVERT: B 167 SER cc_start: 0.8767 (p) cc_final: 0.8416 (t) REVERT: C 210 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8184 (m) REVERT: D 130 SER cc_start: 0.8807 (p) cc_final: 0.8397 (m) REVERT: M 223 ASP cc_start: 0.7094 (t0) cc_final: 0.6750 (t0) REVERT: N 24 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7483 (mp0) REVERT: N 149 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7375 (ttpp) REVERT: N 188 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7814 (m) REVERT: N 344 THR cc_start: 0.8592 (t) cc_final: 0.8236 (p) REVERT: O 24 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7461 (mm-30) REVERT: O 64 TRP cc_start: 0.6962 (p-90) cc_final: 0.6357 (p-90) REVERT: O 87 THR cc_start: 0.7760 (p) cc_final: 0.7239 (t) REVERT: O 179 THR cc_start: 0.8730 (m) cc_final: 0.8393 (p) REVERT: O 195 GLN cc_start: 0.8059 (mt0) cc_final: 0.7764 (mt0) REVERT: O 223 ASP cc_start: 0.8003 (t0) cc_final: 0.7755 (t0) REVERT: O 373 VAL cc_start: 0.8566 (t) cc_final: 0.8306 (m) REVERT: O 382 VAL cc_start: 0.8545 (t) cc_final: 0.8326 (p) REVERT: O 393 ARG cc_start: 0.8106 (ttt90) cc_final: 0.7354 (ttt90) REVERT: P 70 MET cc_start: 0.8237 (tpp) cc_final: 0.7677 (tpp) REVERT: P 181 MET cc_start: 0.7674 (mtt) cc_final: 0.7411 (mtt) REVERT: P 200 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8085 (tttt) REVERT: P 223 ASP cc_start: 0.7153 (t0) cc_final: 0.6913 (t0) REVERT: P 265 THR cc_start: 0.8686 (p) cc_final: 0.8411 (m) REVERT: P 305 ASN cc_start: 0.8078 (m-40) cc_final: 0.7761 (t0) REVERT: R 172 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7919 (mttp) REVERT: S 155 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8159 (pttt) REVERT: S 172 LYS cc_start: 0.7826 (tttt) cc_final: 0.7548 (tmtt) REVERT: T 135 MET cc_start: 0.8685 (mtp) cc_final: 0.8464 (mtp) REVERT: T 205 THR cc_start: 0.7557 (t) cc_final: 0.7174 (m) outliers start: 112 outliers final: 95 residues processed: 715 average time/residue: 0.5317 time to fit residues: 613.7773 Evaluate side-chains 752 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 651 time to evaluate : 4.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 356 ILE Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 153 CYS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 379 LEU Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 347 THR Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 164 CYS Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 251 THR Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 220 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 285 optimal weight: 0.0770 chunk 459 optimal weight: 50.0000 chunk 280 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 482 optimal weight: 20.0000 chunk 443 optimal weight: 6.9990 chunk 383 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 296 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 ASN R 139 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39196 Z= 0.168 Angle : 0.554 10.951 53404 Z= 0.289 Chirality : 0.045 0.354 6036 Planarity : 0.005 0.055 6848 Dihedral : 5.197 58.851 5605 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.09 % Allowed : 16.35 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.79 (0.12), residues: 4916 helix: 1.52 (0.26), residues: 460 sheet: 0.24 (0.12), residues: 1761 loop : -1.48 (0.11), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 330 HIS 0.015 0.001 HIS R 139 PHE 0.029 0.001 PHE C 436 TYR 0.013 0.001 TYR S 160 ARG 0.008 0.000 ARG A 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 651 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.7341 (m-30) cc_final: 0.6843 (p0) REVERT: A 370 CYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6789 (m) REVERT: B 167 SER cc_start: 0.8749 (p) cc_final: 0.8395 (t) REVERT: B 429 ILE cc_start: 0.8515 (mm) cc_final: 0.8242 (tt) REVERT: C 210 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8194 (m) REVERT: C 319 LYS cc_start: 0.7873 (mttt) cc_final: 0.7605 (mttm) REVERT: D 130 SER cc_start: 0.8798 (p) cc_final: 0.8380 (m) REVERT: D 211 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8332 (mmtt) REVERT: M 223 ASP cc_start: 0.7013 (t0) cc_final: 0.6683 (t0) REVERT: N 24 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7432 (mp0) REVERT: N 149 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7265 (ttpp) REVERT: N 188 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7804 (m) REVERT: N 344 THR cc_start: 0.8651 (t) cc_final: 0.8284 (p) REVERT: O 24 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7432 (mm-30) REVERT: O 64 TRP cc_start: 0.6951 (p-90) cc_final: 0.6356 (p-90) REVERT: O 87 THR cc_start: 0.7529 (p) cc_final: 0.7211 (t) REVERT: O 179 THR cc_start: 0.8721 (m) cc_final: 0.8400 (p) REVERT: O 195 GLN cc_start: 0.8009 (mt0) cc_final: 0.7692 (mt0) REVERT: O 223 ASP cc_start: 0.7930 (t0) cc_final: 0.7720 (t0) REVERT: O 366 MET cc_start: 0.6437 (mpp) cc_final: 0.6136 (mpp) REVERT: O 373 VAL cc_start: 0.8471 (t) cc_final: 0.8218 (m) REVERT: O 393 ARG cc_start: 0.8136 (ttt90) cc_final: 0.7546 (ttt180) REVERT: P 70 MET cc_start: 0.8157 (tpp) cc_final: 0.7634 (tpp) REVERT: P 181 MET cc_start: 0.7682 (mtt) cc_final: 0.7431 (mtt) REVERT: P 200 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8066 (tttt) REVERT: P 223 ASP cc_start: 0.7117 (t0) cc_final: 0.6845 (t0) REVERT: P 265 THR cc_start: 0.8695 (p) cc_final: 0.8412 (m) REVERT: P 305 ASN cc_start: 0.7951 (m-40) cc_final: 0.7675 (t0) REVERT: R 172 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7976 (mttp) REVERT: S 155 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8142 (pttt) REVERT: T 135 MET cc_start: 0.8660 (mtp) cc_final: 0.8430 (mtp) REVERT: T 205 THR cc_start: 0.7708 (t) cc_final: 0.7337 (m) REVERT: Y 4 MET cc_start: 0.2624 (ptp) cc_final: 0.2024 (tmm) outliers start: 88 outliers final: 79 residues processed: 700 average time/residue: 0.5331 time to fit residues: 599.8477 Evaluate side-chains 735 residues out of total 4208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 651 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 153 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 236 GLN Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 347 THR Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 251 THR Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 155 LYS Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 304 optimal weight: 0.7980 chunk 409 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 354 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 384 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 394 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 127 HIS P 193 ASN R 139 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119498 restraints weight = 63099.118| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.41 r_work: 0.3272 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39196 Z= 0.148 Angle : 0.534 10.780 53404 Z= 0.277 Chirality : 0.044 0.334 6036 Planarity : 0.005 0.054 6848 Dihedral : 5.072 59.759 5605 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.16 % Allowed : 16.28 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % 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: -0.66 (0.12), residues: 4916 helix: 1.66 (0.26), residues: 460 sheet: 0.36 (0.13), residues: 1721 loop : -1.40 (0.11), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 330 HIS 0.018 0.001 HIS R 139 PHE 0.030 0.001 PHE C 436 TYR 0.022 0.001 TYR S 160 ARG 0.008 0.000 ARG S 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11225.29 seconds wall clock time: 202 minutes 22.66 seconds (12142.66 seconds total)