Starting phenix.real_space_refine on Tue Feb 20 07:32:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6v_14531/02_2024/7z6v_14531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6v_14531/02_2024/7z6v_14531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6v_14531/02_2024/7z6v_14531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6v_14531/02_2024/7z6v_14531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6v_14531/02_2024/7z6v_14531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z6v_14531/02_2024/7z6v_14531.pdb" } resolution = 3.1 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= 0.000 sd= 0.004 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 120 5.16 5 C 17255 2.51 5 N 4445 2.21 5 O 5334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 89": "OE1" <-> "OE2" Residue "X TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 89": "OE1" <-> "OE2" Residue "Y TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27154 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7732 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 8 Chain: "B" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7761 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 49, 'TRANS': 944} Chain breaks: 7 Chain: "C" Number of atoms: 7749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7749 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 7 Chain: "X" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 996 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 996 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "Z" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 996 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "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 Chain: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.64, per 1000 atoms: 0.50 Number of scatterers: 27154 At special positions: 0 Unit cell: (129.32, 136.74, 221.54, 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 120 16.00 O 5334 8.00 N 4445 7.00 C 17255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.09 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.07 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.09 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.10 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.07 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.09 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.10 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.10 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.08 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=1.07 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.86 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.00 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG B1311 " - " ASN B 234 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 122 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 331 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG C1409 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 282 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 10.58 Conformation dependent library (CDL) restraints added in 4.9 seconds 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6266 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 54 sheets defined 25.8% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.935A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.552A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.370A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.785A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.798A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.625A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.004A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.578A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.939A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.019A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.031A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.790A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.273A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.650A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.722A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.065A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.872A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.984A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.004A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.737A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.190A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.637A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.780A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.068A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.643A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.033A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 31 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 111 Processing helix chain 'Y' and resid 28 through 31 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 105 through 111 Processing helix chain 'Z' and resid 28 through 31 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'Z' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.738A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.334A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.437A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.822A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.584A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.458A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.094A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.771A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.780A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.350A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.699A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.105A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.824A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.713A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.724A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.828A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.458A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.095A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.770A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 719 through 727 removed outlier: 5.783A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.699A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.716A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.727A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.622A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.836A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.230A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.303A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.096A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.771A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.221A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.326A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'X' and resid 2 through 7 Processing sheet with id=AF2, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.307A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG X 38 " --> pdb=" O PHE X 47 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N PHE X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.307A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 2 through 7 Processing sheet with id=AF5, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.303A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG Y 38 " --> pdb=" O PHE Y 47 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.303A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 2 through 7 Processing sheet with id=AF8, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.308A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG Z 38 " --> pdb=" O PHE Z 47 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.308A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) 1183 hydrogen bonds defined for protein. 3141 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: 13.16 Time building geometry restraints manager: 11.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4853 1.32 - 1.46: 9956 1.46 - 1.59: 12780 1.59 - 1.73: 1 1.73 - 1.86: 152 Bond restraints: 27742 Sorted by residual: bond pdb=" CA SER C1021 " pdb=" CB SER C1021 " ideal model delta sigma weight residual 1.528 1.455 0.073 1.56e-02 4.11e+03 2.20e+01 bond pdb=" CE1 HIS B 49 " pdb=" NE2 HIS B 49 " ideal model delta sigma weight residual 1.321 1.365 -0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" CA SER A1021 " pdb=" CB SER A1021 " ideal model delta sigma weight residual 1.528 1.460 0.069 1.56e-02 4.11e+03 1.95e+01 bond pdb=" CA SER B1030 " pdb=" CB SER B1030 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.55e-02 4.16e+03 1.87e+01 bond pdb=" CA SER A 721 " pdb=" CB SER A 721 " ideal model delta sigma weight residual 1.532 1.453 0.078 1.82e-02 3.02e+03 1.86e+01 ... (remaining 27737 not shown) Histogram of bond angle deviations from ideal: 93.54 - 101.84: 97 101.84 - 110.13: 6130 110.13 - 118.42: 15937 118.42 - 126.72: 15385 126.72 - 135.01: 169 Bond angle restraints: 37718 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 120.62 -9.92 1.22e+00 6.72e-01 6.61e+01 angle pdb=" N GLN B 901 " pdb=" CA GLN B 901 " pdb=" C GLN B 901 " ideal model delta sigma weight residual 111.14 102.66 8.48 1.08e+00 8.57e-01 6.16e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 119.41 -8.71 1.22e+00 6.72e-01 5.10e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 119.26 -8.56 1.22e+00 6.72e-01 4.93e+01 angle pdb=" CB GLN B 804 " pdb=" CG GLN B 804 " pdb=" CD GLN B 804 " ideal model delta sigma weight residual 112.60 123.77 -11.17 1.70e+00 3.46e-01 4.32e+01 ... (remaining 37713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.60: 16290 21.60 - 43.20: 876 43.20 - 64.80: 116 64.80 - 86.40: 16 86.40 - 108.00: 39 Dihedral angle restraints: 17337 sinusoidal: 7583 harmonic: 9754 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -170.95 84.95 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -18.68 -67.32 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 17334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.541: 4446 0.541 - 1.082: 8 1.082 - 1.622: 0 1.622 - 2.163: 0 2.163 - 2.704: 2 Chirality restraints: 4456 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.11e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.08e+02 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 0.30 -2.70 2.00e-01 2.50e+01 1.83e+02 ... (remaining 4453 not shown) Planarity restraints: 4829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.331 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG F 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.499 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1406 " -0.320 2.00e-02 2.50e+03 2.79e-01 9.76e+02 pdb=" C7 NAG C1406 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG C1406 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG C1406 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG C1406 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.294 2.00e-02 2.50e+03 2.54e-01 8.05e+02 pdb=" C7 NAG A1307 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.058 2.00e-02 2.50e+03 ... (remaining 4826 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 50 2.53 - 3.12: 19829 3.12 - 3.71: 40856 3.71 - 4.31: 64481 4.31 - 4.90: 101992 Nonbonded interactions: 227208 Sorted by model distance: nonbonded pdb=" CA ILE B 101 " pdb=" CD2 LEU B 242 " model vdw 1.932 3.890 nonbonded pdb=" CG1 ILE B 101 " pdb=" CD2 LEU B 242 " model vdw 1.957 3.860 nonbonded pdb=" O TRP X 53 " pdb=" CZ ARG X 72 " model vdw 1.963 3.270 nonbonded pdb=" O TRP Y 53 " pdb=" CZ ARG Y 72 " model vdw 1.964 3.270 nonbonded pdb=" O TRP Z 53 " pdb=" CZ ARG Z 72 " model vdw 1.965 3.270 ... (remaining 227203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 263 or resid 265 through 676 or resid 690 through 827 or resid 855 through 1147 \ or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 211 or resid 215 through 263 or resid 265 through 1147 or resid 1301 through 13 \ 08)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 211 or resid 215 through 1147 or resid 1401 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.080 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 72.980 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.010 0.097 27742 Z= 0.648 Angle : 1.644 16.179 37718 Z= 1.068 Chirality : 0.137 2.704 4456 Planarity : 0.020 0.283 4782 Dihedral : 13.892 107.998 10948 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 0.45 % Allowed : 7.18 % Favored : 92.37 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 3304 helix: 0.98 (0.18), residues: 682 sheet: 0.29 (0.17), residues: 803 loop : -0.72 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP B 104 HIS 0.025 0.007 HIS B 655 PHE 0.062 0.010 PHE B 565 TYR 0.053 0.009 TYR B 741 ARG 0.031 0.003 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 519 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7807 (mttm) cc_final: 0.7492 (mppt) REVERT: A 65 PHE cc_start: 0.8216 (m-80) cc_final: 0.7880 (m-80) REVERT: A 133 PHE cc_start: 0.6701 (m-80) cc_final: 0.6228 (t80) REVERT: A 136 CYS cc_start: 0.6402 (m) cc_final: 0.6149 (t) REVERT: A 137 ASN cc_start: 0.6847 (m-40) cc_final: 0.6482 (p0) REVERT: A 169 GLU cc_start: 0.8473 (tt0) cc_final: 0.8068 (tm-30) REVERT: A 200 TYR cc_start: 0.5633 (p90) cc_final: 0.5093 (p90) REVERT: A 343 ASN cc_start: 0.4843 (m-40) cc_final: 0.4272 (t0) REVERT: A 568 ASP cc_start: 0.8472 (t0) cc_final: 0.8118 (p0) REVERT: A 697 MET cc_start: 0.9103 (ptm) cc_final: 0.8856 (ptm) REVERT: A 702 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8395 (mm-30) REVERT: A 811 LYS cc_start: 0.5386 (mttt) cc_final: 0.5083 (tttm) REVERT: A 825 LYS cc_start: 0.8279 (mmtt) cc_final: 0.8056 (mmmt) REVERT: A 859 THR cc_start: 0.9221 (p) cc_final: 0.8833 (t) REVERT: A 1045 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8721 (mmtm) REVERT: A 1113 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8664 (mt0) REVERT: B 117 LEU cc_start: 0.7671 (tp) cc_final: 0.7017 (mp) REVERT: B 129 LYS cc_start: 0.7202 (mttt) cc_final: 0.6913 (pttp) REVERT: B 131 CYS cc_start: 0.6812 (m) cc_final: 0.6521 (t) REVERT: B 191 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8259 (mt-10) REVERT: B 235 ILE cc_start: 0.7046 (mt) cc_final: 0.6540 (mm) REVERT: B 357 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8226 (ttm170) REVERT: B 403 ARG cc_start: 0.7052 (ptt180) cc_final: 0.6460 (ptt-90) REVERT: B 427 ASP cc_start: 0.8047 (m-30) cc_final: 0.7544 (m-30) REVERT: B 449 TYR cc_start: 0.6693 (m-80) cc_final: 0.6467 (m-80) REVERT: B 453 TYR cc_start: 0.7581 (p90) cc_final: 0.7174 (p90) REVERT: B 535 LYS cc_start: 0.8420 (mttt) cc_final: 0.8138 (mtmt) REVERT: B 558 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7616 (mttt) REVERT: B 586 ASP cc_start: 0.8096 (m-30) cc_final: 0.7865 (t0) REVERT: B 661 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8597 (tt0) REVERT: B 675 GLN cc_start: 0.7833 (mt0) cc_final: 0.7449 (pp30) REVERT: B 745 ASP cc_start: 0.7800 (m-30) cc_final: 0.7582 (t70) REVERT: B 755 GLN cc_start: 0.8747 (mt0) cc_final: 0.8381 (mm-40) REVERT: B 868 GLU cc_start: 0.8389 (pp20) cc_final: 0.8104 (mm-30) REVERT: B 985 ASP cc_start: 0.7691 (m-30) cc_final: 0.7143 (p0) REVERT: B 1073 LYS cc_start: 0.8609 (mttt) cc_final: 0.8392 (mtpp) REVERT: B 1081 ILE cc_start: 0.9069 (pt) cc_final: 0.8862 (pt) REVERT: B 1092 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8583 (pt0) REVERT: C 85 PRO cc_start: 0.7383 (Cg_exo) cc_final: 0.7162 (Cg_endo) REVERT: C 113 LYS cc_start: 0.6827 (mttm) cc_final: 0.6601 (tptp) REVERT: C 198 ASP cc_start: 0.8158 (m-30) cc_final: 0.7633 (p0) REVERT: C 353 TRP cc_start: 0.5665 (p-90) cc_final: 0.5285 (p-90) REVERT: C 360 ASN cc_start: 0.8389 (t0) cc_final: 0.8063 (m-40) REVERT: C 364 ASP cc_start: 0.8358 (t0) cc_final: 0.8139 (t70) REVERT: C 378 LYS cc_start: 0.7303 (tttt) cc_final: 0.6953 (tptp) REVERT: C 380 TYR cc_start: 0.8058 (m-80) cc_final: 0.7579 (m-80) REVERT: C 433 VAL cc_start: 0.7662 (t) cc_final: 0.7147 (m) REVERT: C 532 ASN cc_start: 0.8579 (t0) cc_final: 0.7961 (m110) REVERT: C 646 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8434 (tpt-90) REVERT: C 675 GLN cc_start: 0.8264 (mt0) cc_final: 0.7342 (pp30) REVERT: C 734 THR cc_start: 0.9022 (m) cc_final: 0.8628 (p) REVERT: C 745 ASP cc_start: 0.8076 (m-30) cc_final: 0.7789 (p0) REVERT: C 868 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8386 (mp0) REVERT: C 869 MET cc_start: 0.9235 (mtt) cc_final: 0.8974 (mtp) REVERT: C 950 ASP cc_start: 0.8779 (t70) cc_final: 0.8317 (m-30) REVERT: C 960 ASN cc_start: 0.8305 (m-40) cc_final: 0.7978 (t0) REVERT: C 985 ASP cc_start: 0.7639 (m-30) cc_final: 0.7184 (p0) REVERT: C 1045 LYS cc_start: 0.9192 (mttt) cc_final: 0.8413 (tmtt) REVERT: C 1081 ILE cc_start: 0.9061 (pt) cc_final: 0.8735 (mt) REVERT: Y 85 SER cc_start: 0.4982 (m) cc_final: 0.4774 (p) REVERT: Y 103 ARG cc_start: 0.7383 (mmm160) cc_final: 0.6487 (mmm-85) REVERT: Z 34 MET cc_start: 0.1237 (mmm) cc_final: 0.0969 (ptp) outliers start: 13 outliers final: 3 residues processed: 529 average time/residue: 0.4127 time to fit residues: 334.4754 Evaluate side-chains 298 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 295 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 87 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 302 optimal weight: 20.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 239 GLN A 334 ASN A 901 GLN A 907 ASN A 914 ASN A 954 GLN A1048 HIS A1054 GLN A1113 GLN B 121 ASN B 207 HIS B 271 GLN B 360 ASN B 388 ASN B 607 GLN B 690 GLN B 762 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1010 GLN B1011 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 207 HIS C 388 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 787 GLN C 901 GLN C 957 GLN C1010 GLN C1011 GLN C1036 GLN C1048 HIS C1054 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27742 Z= 0.235 Angle : 0.620 12.290 37718 Z= 0.319 Chirality : 0.046 0.296 4456 Planarity : 0.004 0.040 4782 Dihedral : 7.983 95.054 5003 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 1.44 % Allowed : 9.86 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3304 helix: 1.97 (0.20), residues: 675 sheet: 0.63 (0.17), residues: 812 loop : -0.49 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 PHE 0.023 0.002 PHE B 192 TYR 0.021 0.001 TYR B1067 ARG 0.008 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 328 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8901 (p) cc_final: 0.8694 (p) REVERT: A 41 LYS cc_start: 0.7885 (mttm) cc_final: 0.7669 (mmtm) REVERT: A 65 PHE cc_start: 0.8224 (m-80) cc_final: 0.7731 (m-80) REVERT: A 102 ARG cc_start: 0.6452 (mmt180) cc_final: 0.6188 (mmp-170) REVERT: A 133 PHE cc_start: 0.7151 (m-80) cc_final: 0.6530 (t80) REVERT: A 136 CYS cc_start: 0.6291 (m) cc_final: 0.6046 (t) REVERT: A 137 ASN cc_start: 0.6838 (m-40) cc_final: 0.6437 (p0) REVERT: A 169 GLU cc_start: 0.8414 (tt0) cc_final: 0.7982 (tm-30) REVERT: A 200 TYR cc_start: 0.5899 (p90) cc_final: 0.5311 (p90) REVERT: A 343 ASN cc_start: 0.4887 (m-40) cc_final: 0.4257 (t0) REVERT: A 400 PHE cc_start: 0.5982 (p90) cc_final: 0.5761 (p90) REVERT: A 568 ASP cc_start: 0.8554 (t0) cc_final: 0.8306 (m-30) REVERT: A 697 MET cc_start: 0.9041 (ptm) cc_final: 0.8682 (ptm) REVERT: A 811 LYS cc_start: 0.5637 (mttt) cc_final: 0.5238 (tttm) REVERT: A 1045 LYS cc_start: 0.9286 (mmtt) cc_final: 0.8724 (mmtm) REVERT: A 1113 GLN cc_start: 0.8945 (mm110) cc_final: 0.8683 (mt0) REVERT: B 129 LYS cc_start: 0.7205 (mttt) cc_final: 0.6911 (pttp) REVERT: B 235 ILE cc_start: 0.7051 (mt) cc_final: 0.6626 (mm) REVERT: B 357 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8178 (ttt180) REVERT: B 403 ARG cc_start: 0.6867 (ptt180) cc_final: 0.6343 (ptt180) REVERT: B 453 TYR cc_start: 0.7621 (p90) cc_final: 0.7355 (p90) REVERT: B 554 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8450 (pp20) REVERT: B 558 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7747 (mttm) REVERT: B 616 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7089 (m-40) REVERT: B 661 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8506 (tt0) REVERT: B 675 GLN cc_start: 0.7830 (mt0) cc_final: 0.7430 (pp30) REVERT: B 745 ASP cc_start: 0.7906 (m-30) cc_final: 0.7703 (t0) REVERT: B 902 MET cc_start: 0.8956 (mmm) cc_final: 0.8752 (mmm) REVERT: B 985 ASP cc_start: 0.7760 (m-30) cc_final: 0.7241 (p0) REVERT: B 988 GLU cc_start: 0.8240 (mp0) cc_final: 0.7931 (mt-10) REVERT: B 1073 LYS cc_start: 0.8467 (mttt) cc_final: 0.8182 (mtpt) REVERT: B 1092 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8558 (pt0) REVERT: C 113 LYS cc_start: 0.6733 (mttm) cc_final: 0.6494 (tptp) REVERT: C 198 ASP cc_start: 0.8273 (m-30) cc_final: 0.7980 (m-30) REVERT: C 239 GLN cc_start: 0.8118 (pt0) cc_final: 0.7664 (mt0) REVERT: C 353 TRP cc_start: 0.5651 (p-90) cc_final: 0.5321 (p-90) REVERT: C 360 ASN cc_start: 0.8438 (t0) cc_final: 0.8153 (m-40) REVERT: C 378 LYS cc_start: 0.7400 (tttt) cc_final: 0.7003 (tptp) REVERT: C 380 TYR cc_start: 0.8224 (m-80) cc_final: 0.7938 (m-80) REVERT: C 396 TYR cc_start: 0.7793 (m-80) cc_final: 0.7440 (m-80) REVERT: C 646 ARG cc_start: 0.8877 (tpp80) cc_final: 0.8420 (tpt-90) REVERT: C 675 GLN cc_start: 0.8309 (mt0) cc_final: 0.7307 (pp30) REVERT: C 734 THR cc_start: 0.9155 (m) cc_final: 0.8765 (p) REVERT: C 758 SER cc_start: 0.8855 (p) cc_final: 0.8626 (p) REVERT: C 868 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8354 (mp0) REVERT: C 869 MET cc_start: 0.9166 (mtt) cc_final: 0.8740 (mtp) REVERT: C 950 ASP cc_start: 0.8795 (t70) cc_final: 0.8285 (m-30) REVERT: C 960 ASN cc_start: 0.8302 (m-40) cc_final: 0.8100 (t0) REVERT: C 985 ASP cc_start: 0.7837 (m-30) cc_final: 0.7328 (p0) REVERT: C 1010 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8142 (pt0) REVERT: C 1045 LYS cc_start: 0.9032 (mttt) cc_final: 0.8239 (tmtt) REVERT: C 1081 ILE cc_start: 0.8986 (pt) cc_final: 0.8654 (mt) REVERT: Y 85 SER cc_start: 0.5084 (m) cc_final: 0.4884 (p) REVERT: Y 103 ARG cc_start: 0.7424 (mmm160) cc_final: 0.6836 (mmm160) REVERT: Z 34 MET cc_start: 0.0873 (mmm) cc_final: 0.0464 (ptp) outliers start: 42 outliers final: 22 residues processed: 356 average time/residue: 0.4023 time to fit residues: 227.7517 Evaluate side-chains 286 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 262 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 251 optimal weight: 0.7980 chunk 205 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 302 optimal weight: 8.9990 chunk 327 optimal weight: 10.0000 chunk 269 optimal weight: 0.8980 chunk 300 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 243 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 544 ASN A 779 GLN B 370 ASN B 901 GLN B 914 ASN B1048 HIS B1106 GLN C 66 HIS C 207 HIS C1054 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27742 Z= 0.170 Angle : 0.529 10.142 37718 Z= 0.272 Chirality : 0.044 0.256 4456 Planarity : 0.003 0.038 4782 Dihedral : 6.429 85.130 4996 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.91 % Rotamer: Outliers : 1.37 % Allowed : 10.79 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3304 helix: 2.10 (0.20), residues: 683 sheet: 0.60 (0.17), residues: 848 loop : -0.36 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 PHE 0.017 0.001 PHE B 456 TYR 0.026 0.001 TYR B 380 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 303 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8850 (p) cc_final: 0.8646 (p) REVERT: A 65 PHE cc_start: 0.8148 (m-80) cc_final: 0.7660 (m-80) REVERT: A 133 PHE cc_start: 0.7364 (m-80) cc_final: 0.6261 (t80) REVERT: A 136 CYS cc_start: 0.6535 (m) cc_final: 0.6316 (t) REVERT: A 137 ASN cc_start: 0.6842 (m-40) cc_final: 0.6431 (p0) REVERT: A 169 GLU cc_start: 0.8464 (tt0) cc_final: 0.8059 (tm-30) REVERT: A 200 TYR cc_start: 0.5924 (p90) cc_final: 0.5331 (p90) REVERT: A 343 ASN cc_start: 0.4987 (m-40) cc_final: 0.4344 (t0) REVERT: A 400 PHE cc_start: 0.6083 (p90) cc_final: 0.5837 (p90) REVERT: A 697 MET cc_start: 0.9026 (ptm) cc_final: 0.8628 (ptm) REVERT: A 735 SER cc_start: 0.9016 (t) cc_final: 0.8729 (p) REVERT: A 811 LYS cc_start: 0.6032 (mttt) cc_final: 0.5557 (tttm) REVERT: A 868 GLU cc_start: 0.8475 (mp0) cc_final: 0.8079 (tt0) REVERT: A 1045 LYS cc_start: 0.9261 (mmtt) cc_final: 0.8669 (mmtm) REVERT: A 1113 GLN cc_start: 0.8924 (mm110) cc_final: 0.8691 (mt0) REVERT: B 117 LEU cc_start: 0.7683 (tp) cc_final: 0.7032 (mp) REVERT: B 235 ILE cc_start: 0.7060 (mt) cc_final: 0.6450 (mm) REVERT: B 316 SER cc_start: 0.8451 (t) cc_final: 0.8110 (m) REVERT: B 403 ARG cc_start: 0.7007 (ptt180) cc_final: 0.6499 (ptt180) REVERT: B 554 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8395 (pp20) REVERT: B 675 GLN cc_start: 0.7870 (mt0) cc_final: 0.7440 (pp30) REVERT: B 735 SER cc_start: 0.8710 (t) cc_final: 0.8474 (p) REVERT: B 745 ASP cc_start: 0.7987 (m-30) cc_final: 0.7710 (t0) REVERT: B 780 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8580 (tt0) REVERT: B 985 ASP cc_start: 0.7687 (m-30) cc_final: 0.7115 (p0) REVERT: B 988 GLU cc_start: 0.8248 (mp0) cc_final: 0.7885 (mt-10) REVERT: B 1073 LYS cc_start: 0.8438 (mttt) cc_final: 0.8153 (mtpt) REVERT: B 1081 ILE cc_start: 0.8759 (pt) cc_final: 0.8503 (mt) REVERT: B 1092 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8634 (pt0) REVERT: B 1106 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8933 (pm20) REVERT: C 191 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8019 (mm-30) REVERT: C 198 ASP cc_start: 0.8284 (m-30) cc_final: 0.8000 (m-30) REVERT: C 239 GLN cc_start: 0.8279 (pt0) cc_final: 0.7880 (tt0) REVERT: C 305 SER cc_start: 0.9303 (t) cc_final: 0.9008 (p) REVERT: C 351 TYR cc_start: 0.6458 (p90) cc_final: 0.5955 (p90) REVERT: C 353 TRP cc_start: 0.5680 (p-90) cc_final: 0.5465 (p-90) REVERT: C 360 ASN cc_start: 0.8463 (t0) cc_final: 0.8164 (m-40) REVERT: C 378 LYS cc_start: 0.7501 (tttt) cc_final: 0.7219 (mmmt) REVERT: C 380 TYR cc_start: 0.8329 (m-80) cc_final: 0.8071 (m-80) REVERT: C 388 ASN cc_start: 0.7897 (m110) cc_final: 0.7431 (t0) REVERT: C 646 ARG cc_start: 0.8888 (tpp80) cc_final: 0.8415 (tpt-90) REVERT: C 675 GLN cc_start: 0.8323 (mt0) cc_final: 0.7357 (pp30) REVERT: C 734 THR cc_start: 0.9159 (m) cc_final: 0.8799 (p) REVERT: C 786 LYS cc_start: 0.7953 (mttt) cc_final: 0.7711 (mtmm) REVERT: C 868 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8340 (mp0) REVERT: C 869 MET cc_start: 0.9181 (mtt) cc_final: 0.8764 (mtp) REVERT: C 950 ASP cc_start: 0.8745 (t70) cc_final: 0.8197 (m-30) REVERT: C 960 ASN cc_start: 0.8327 (m-40) cc_final: 0.8115 (t0) REVERT: C 985 ASP cc_start: 0.7718 (m-30) cc_final: 0.7232 (p0) REVERT: C 1010 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8115 (pt0) REVERT: C 1045 LYS cc_start: 0.8892 (mttt) cc_final: 0.8108 (tmtt) REVERT: C 1081 ILE cc_start: 0.8873 (pt) cc_final: 0.8599 (mt) REVERT: Y 85 SER cc_start: 0.5227 (m) cc_final: 0.5021 (p) REVERT: Y 103 ARG cc_start: 0.7488 (mmm160) cc_final: 0.6891 (mmm160) REVERT: Z 34 MET cc_start: 0.0974 (mmm) cc_final: 0.0466 (ptp) outliers start: 40 outliers final: 25 residues processed: 328 average time/residue: 0.4092 time to fit residues: 213.6113 Evaluate side-chains 283 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 256 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 299 optimal weight: 20.0000 chunk 227 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 288 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 394 ASN B 675 GLN B1106 GLN C 66 HIS C 613 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27742 Z= 0.275 Angle : 0.546 7.552 37718 Z= 0.281 Chirality : 0.045 0.373 4456 Planarity : 0.004 0.043 4782 Dihedral : 5.820 71.385 4996 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Rotamer: Outliers : 1.96 % Allowed : 11.23 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3304 helix: 2.05 (0.20), residues: 662 sheet: 0.51 (0.17), residues: 860 loop : -0.31 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 PHE 0.017 0.001 PHE C 898 TYR 0.026 0.001 TYR B 380 ARG 0.006 0.000 ARG X 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 278 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8161 (m-80) cc_final: 0.7696 (m-80) REVERT: A 133 PHE cc_start: 0.7464 (m-80) cc_final: 0.6258 (t80) REVERT: A 136 CYS cc_start: 0.6556 (m) cc_final: 0.6314 (t) REVERT: A 137 ASN cc_start: 0.6835 (m-40) cc_final: 0.6441 (p0) REVERT: A 169 GLU cc_start: 0.8543 (tt0) cc_final: 0.8126 (tm-30) REVERT: A 200 TYR cc_start: 0.6165 (p90) cc_final: 0.5448 (p90) REVERT: A 309 GLU cc_start: 0.8422 (pm20) cc_final: 0.7769 (mt-10) REVERT: A 334 ASN cc_start: 0.6818 (t0) cc_final: 0.6586 (t0) REVERT: A 343 ASN cc_start: 0.5208 (m-40) cc_final: 0.4599 (t0) REVERT: A 400 PHE cc_start: 0.6219 (p90) cc_final: 0.6005 (p90) REVERT: A 697 MET cc_start: 0.9056 (ptm) cc_final: 0.8651 (ptm) REVERT: A 735 SER cc_start: 0.9022 (t) cc_final: 0.8688 (p) REVERT: A 1113 GLN cc_start: 0.8993 (mm110) cc_final: 0.8681 (mt0) REVERT: B 53 ASP cc_start: 0.8117 (t0) cc_final: 0.7848 (t0) REVERT: B 117 LEU cc_start: 0.7716 (tp) cc_final: 0.6989 (mp) REVERT: B 237 ARG cc_start: 0.7328 (mtp85) cc_final: 0.7104 (mtp85) REVERT: B 287 ASP cc_start: 0.8640 (t0) cc_final: 0.8155 (m-30) REVERT: B 378 LYS cc_start: 0.7941 (tttt) cc_final: 0.7477 (mmtp) REVERT: B 403 ARG cc_start: 0.7086 (ptt180) cc_final: 0.6532 (ptt180) REVERT: B 554 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8362 (pp20) REVERT: B 616 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7120 (m-40) REVERT: B 675 GLN cc_start: 0.7943 (mt0) cc_final: 0.7494 (pp30) REVERT: B 745 ASP cc_start: 0.7980 (m-30) cc_final: 0.7713 (t0) REVERT: B 780 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8657 (tt0) REVERT: B 985 ASP cc_start: 0.7803 (m-30) cc_final: 0.7141 (p0) REVERT: B 987 PRO cc_start: 0.8363 (Cg_exo) cc_final: 0.7888 (Cg_endo) REVERT: B 988 GLU cc_start: 0.8287 (mp0) cc_final: 0.7833 (mt-10) REVERT: B 1073 LYS cc_start: 0.8646 (mttt) cc_final: 0.8335 (mtpt) REVERT: B 1092 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8649 (pt0) REVERT: C 191 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8153 (mm-30) REVERT: C 198 ASP cc_start: 0.8286 (m-30) cc_final: 0.8075 (m-30) REVERT: C 239 GLN cc_start: 0.8294 (pt0) cc_final: 0.7601 (mt0) REVERT: C 305 SER cc_start: 0.9290 (t) cc_final: 0.8985 (p) REVERT: C 351 TYR cc_start: 0.6468 (p90) cc_final: 0.5978 (p90) REVERT: C 360 ASN cc_start: 0.8506 (t0) cc_final: 0.8204 (m-40) REVERT: C 378 LYS cc_start: 0.7494 (tttt) cc_final: 0.7177 (mmmt) REVERT: C 380 TYR cc_start: 0.8338 (m-80) cc_final: 0.8061 (m-80) REVERT: C 646 ARG cc_start: 0.8903 (tpp80) cc_final: 0.8412 (tpt-90) REVERT: C 675 GLN cc_start: 0.8386 (mt0) cc_final: 0.7415 (pp30) REVERT: C 734 THR cc_start: 0.9140 (m) cc_final: 0.8807 (p) REVERT: C 868 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8383 (mp0) REVERT: C 869 MET cc_start: 0.9168 (mtt) cc_final: 0.8924 (mtp) REVERT: C 950 ASP cc_start: 0.8771 (t70) cc_final: 0.8251 (m-30) REVERT: C 960 ASN cc_start: 0.8365 (m-40) cc_final: 0.8072 (t0) REVERT: C 985 ASP cc_start: 0.7758 (m-30) cc_final: 0.7275 (p0) REVERT: C 1010 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8181 (pt0) REVERT: C 1045 LYS cc_start: 0.8955 (mttt) cc_final: 0.8208 (tmtt) REVERT: C 1081 ILE cc_start: 0.8904 (pt) cc_final: 0.8608 (mt) REVERT: X 34 MET cc_start: 0.1255 (ptp) cc_final: -0.0066 (tpt) REVERT: Y 103 ARG cc_start: 0.7406 (mmm160) cc_final: 0.6830 (mmm160) REVERT: Z 34 MET cc_start: 0.0857 (mmm) cc_final: 0.0377 (ptp) outliers start: 57 outliers final: 42 residues processed: 315 average time/residue: 0.3789 time to fit residues: 192.4173 Evaluate side-chains 299 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 255 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 0.0070 chunk 182 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 222 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 0.6980 chunk 288 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 544 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 207 HIS C 913 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27742 Z= 0.197 Angle : 0.505 8.196 37718 Z= 0.260 Chirality : 0.043 0.253 4456 Planarity : 0.003 0.044 4782 Dihedral : 5.392 61.522 4996 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.12 % Favored : 97.85 % Rotamer: Outliers : 1.72 % Allowed : 12.33 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3304 helix: 2.19 (0.20), residues: 663 sheet: 0.61 (0.17), residues: 825 loop : -0.29 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 PHE 0.016 0.001 PHE B 456 TYR 0.021 0.001 TYR B 453 ARG 0.006 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 277 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8154 (m-80) cc_final: 0.7713 (m-80) REVERT: A 133 PHE cc_start: 0.7419 (m-80) cc_final: 0.6108 (t80) REVERT: A 136 CYS cc_start: 0.6635 (m) cc_final: 0.6358 (t) REVERT: A 137 ASN cc_start: 0.6760 (m-40) cc_final: 0.6364 (p0) REVERT: A 169 GLU cc_start: 0.8540 (tt0) cc_final: 0.8112 (tm-30) REVERT: A 200 TYR cc_start: 0.6209 (p90) cc_final: 0.5494 (p90) REVERT: A 309 GLU cc_start: 0.8428 (pm20) cc_final: 0.7792 (mt-10) REVERT: A 334 ASN cc_start: 0.6840 (t0) cc_final: 0.6568 (t0) REVERT: A 343 ASN cc_start: 0.5232 (m-40) cc_final: 0.4599 (t0) REVERT: A 400 PHE cc_start: 0.6202 (p90) cc_final: 0.5988 (p90) REVERT: A 697 MET cc_start: 0.9059 (ptm) cc_final: 0.8695 (ptm) REVERT: A 735 SER cc_start: 0.8997 (t) cc_final: 0.8666 (p) REVERT: A 1113 GLN cc_start: 0.8985 (mm110) cc_final: 0.8706 (mt0) REVERT: B 41 LYS cc_start: 0.6950 (pttt) cc_final: 0.6732 (ptpp) REVERT: B 53 ASP cc_start: 0.8125 (t0) cc_final: 0.7861 (t0) REVERT: B 117 LEU cc_start: 0.7638 (tp) cc_final: 0.6909 (mp) REVERT: B 235 ILE cc_start: 0.7010 (mt) cc_final: 0.6441 (mm) REVERT: B 237 ARG cc_start: 0.7305 (mtp85) cc_final: 0.7086 (mtp85) REVERT: B 287 ASP cc_start: 0.8615 (t0) cc_final: 0.8128 (m-30) REVERT: B 403 ARG cc_start: 0.7089 (ptt180) cc_final: 0.6520 (ptt180) REVERT: B 554 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8316 (pp20) REVERT: B 616 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7015 (m-40) REVERT: B 675 GLN cc_start: 0.8008 (mt0) cc_final: 0.7584 (pp30) REVERT: B 745 ASP cc_start: 0.8052 (m-30) cc_final: 0.7771 (t70) REVERT: B 780 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8719 (tt0) REVERT: B 985 ASP cc_start: 0.7728 (m-30) cc_final: 0.7072 (p0) REVERT: B 987 PRO cc_start: 0.8319 (Cg_exo) cc_final: 0.7819 (Cg_endo) REVERT: B 988 GLU cc_start: 0.8216 (mp0) cc_final: 0.7739 (mt-10) REVERT: B 1073 LYS cc_start: 0.8640 (mttt) cc_final: 0.8329 (mtpt) REVERT: B 1081 ILE cc_start: 0.8705 (pt) cc_final: 0.8483 (mt) REVERT: B 1092 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8618 (pt0) REVERT: C 191 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8219 (mm-30) REVERT: C 239 GLN cc_start: 0.8356 (pt0) cc_final: 0.7853 (mt0) REVERT: C 305 SER cc_start: 0.9290 (t) cc_final: 0.9004 (p) REVERT: C 351 TYR cc_start: 0.6517 (p90) cc_final: 0.6048 (p90) REVERT: C 359 SER cc_start: 0.8270 (p) cc_final: 0.7932 (m) REVERT: C 360 ASN cc_start: 0.8528 (t0) cc_final: 0.8216 (m-40) REVERT: C 378 LYS cc_start: 0.7494 (tttt) cc_final: 0.7194 (mmmt) REVERT: C 380 TYR cc_start: 0.8416 (m-80) cc_final: 0.8167 (m-80) REVERT: C 388 ASN cc_start: 0.8037 (m110) cc_final: 0.7776 (t0) REVERT: C 565 PHE cc_start: 0.7355 (p90) cc_final: 0.7035 (p90) REVERT: C 646 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8401 (tpt-90) REVERT: C 675 GLN cc_start: 0.8397 (mt0) cc_final: 0.7431 (pp30) REVERT: C 734 THR cc_start: 0.9138 (m) cc_final: 0.8772 (p) REVERT: C 868 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8395 (mp0) REVERT: C 869 MET cc_start: 0.9193 (mtt) cc_final: 0.8768 (mtp) REVERT: C 950 ASP cc_start: 0.8724 (t70) cc_final: 0.8211 (m-30) REVERT: C 960 ASN cc_start: 0.8345 (m-40) cc_final: 0.8081 (t0) REVERT: C 985 ASP cc_start: 0.7760 (m-30) cc_final: 0.7269 (p0) REVERT: C 1010 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8181 (pt0) REVERT: C 1045 LYS cc_start: 0.8897 (mttt) cc_final: 0.8497 (tptt) REVERT: C 1081 ILE cc_start: 0.8841 (pt) cc_final: 0.8581 (mt) REVERT: X 34 MET cc_start: 0.1150 (ptp) cc_final: -0.0351 (tpp) REVERT: Y 103 ARG cc_start: 0.7425 (mmm160) cc_final: 0.6917 (mmm160) REVERT: Z 34 MET cc_start: 0.0781 (mmm) cc_final: 0.0565 (ptp) outliers start: 50 outliers final: 32 residues processed: 312 average time/residue: 0.3852 time to fit residues: 194.3761 Evaluate side-chains 296 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 262 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 108 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 322 optimal weight: 20.0000 chunk 267 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 239 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 955 ASN C 207 HIS C1054 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27742 Z= 0.191 Angle : 0.497 8.668 37718 Z= 0.256 Chirality : 0.043 0.247 4456 Planarity : 0.003 0.044 4782 Dihedral : 5.025 53.897 4996 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.72 % Allowed : 12.44 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3304 helix: 2.29 (0.20), residues: 658 sheet: 0.59 (0.17), residues: 839 loop : -0.25 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 PHE 0.018 0.001 PHE C 643 TYR 0.019 0.001 TYR B 453 ARG 0.006 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 271 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8149 (m-80) cc_final: 0.7741 (m-80) REVERT: A 133 PHE cc_start: 0.7467 (m-80) cc_final: 0.6269 (t80) REVERT: A 136 CYS cc_start: 0.6478 (m) cc_final: 0.6212 (t) REVERT: A 137 ASN cc_start: 0.6812 (m-40) cc_final: 0.6409 (p0) REVERT: A 169 GLU cc_start: 0.8570 (tt0) cc_final: 0.8153 (tm-30) REVERT: A 200 TYR cc_start: 0.6247 (p90) cc_final: 0.5497 (p90) REVERT: A 309 GLU cc_start: 0.8453 (pm20) cc_final: 0.7812 (mt-10) REVERT: A 343 ASN cc_start: 0.5192 (m-40) cc_final: 0.4594 (t0) REVERT: A 735 SER cc_start: 0.9004 (t) cc_final: 0.8664 (p) REVERT: A 1113 GLN cc_start: 0.8992 (mm110) cc_final: 0.8723 (mt0) REVERT: B 41 LYS cc_start: 0.6963 (pttt) cc_final: 0.6739 (ptpp) REVERT: B 117 LEU cc_start: 0.7593 (tp) cc_final: 0.6804 (mp) REVERT: B 287 ASP cc_start: 0.8616 (t0) cc_final: 0.8132 (m-30) REVERT: B 378 LYS cc_start: 0.7874 (tttt) cc_final: 0.7379 (mmtp) REVERT: B 380 TYR cc_start: 0.8179 (m-10) cc_final: 0.7861 (m-80) REVERT: B 403 ARG cc_start: 0.6930 (ptt180) cc_final: 0.6358 (ptt180) REVERT: B 554 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8298 (pp20) REVERT: B 675 GLN cc_start: 0.8070 (mt0) cc_final: 0.7547 (pp30) REVERT: B 745 ASP cc_start: 0.8212 (m-30) cc_final: 0.7915 (t70) REVERT: B 1073 LYS cc_start: 0.8635 (mttt) cc_final: 0.8158 (mptt) REVERT: B 1081 ILE cc_start: 0.8731 (pt) cc_final: 0.8511 (mt) REVERT: B 1092 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8599 (pt0) REVERT: C 191 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8253 (mm-30) REVERT: C 239 GLN cc_start: 0.8352 (pt0) cc_final: 0.7835 (mt0) REVERT: C 305 SER cc_start: 0.9285 (t) cc_final: 0.9009 (p) REVERT: C 351 TYR cc_start: 0.6512 (p90) cc_final: 0.6012 (p90) REVERT: C 359 SER cc_start: 0.8334 (p) cc_final: 0.7962 (m) REVERT: C 360 ASN cc_start: 0.8564 (t0) cc_final: 0.8240 (m-40) REVERT: C 378 LYS cc_start: 0.7488 (tttt) cc_final: 0.7184 (mmmt) REVERT: C 380 TYR cc_start: 0.8419 (m-80) cc_final: 0.8192 (m-80) REVERT: C 388 ASN cc_start: 0.8058 (m110) cc_final: 0.7756 (t0) REVERT: C 565 PHE cc_start: 0.7296 (p90) cc_final: 0.6986 (p90) REVERT: C 646 ARG cc_start: 0.8896 (tpp80) cc_final: 0.8409 (tpt-90) REVERT: C 675 GLN cc_start: 0.8408 (mt0) cc_final: 0.7453 (pp30) REVERT: C 734 THR cc_start: 0.9125 (m) cc_final: 0.8794 (p) REVERT: C 868 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8407 (mp0) REVERT: C 869 MET cc_start: 0.9195 (mtt) cc_final: 0.8769 (mtp) REVERT: C 950 ASP cc_start: 0.8708 (t70) cc_final: 0.8167 (m-30) REVERT: C 960 ASN cc_start: 0.8347 (m-40) cc_final: 0.8080 (t0) REVERT: C 985 ASP cc_start: 0.7765 (m-30) cc_final: 0.7265 (p0) REVERT: C 1010 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8194 (pt0) REVERT: C 1045 LYS cc_start: 0.8907 (mttt) cc_final: 0.8502 (tptt) REVERT: C 1081 ILE cc_start: 0.8816 (pt) cc_final: 0.8573 (mt) REVERT: Y 103 ARG cc_start: 0.7427 (mmm160) cc_final: 0.6906 (mmm160) REVERT: Z 34 MET cc_start: 0.0914 (mmm) cc_final: 0.0689 (ptp) outliers start: 50 outliers final: 36 residues processed: 305 average time/residue: 0.3775 time to fit residues: 186.4149 Evaluate side-chains 295 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 258 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 310 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 320 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 334 ASN A 450 ASN A 613 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 125 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 450 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 27742 Z= 0.434 Angle : 0.614 10.974 37718 Z= 0.310 Chirality : 0.047 0.437 4456 Planarity : 0.004 0.041 4782 Dihedral : 5.329 52.771 4996 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 1.79 % Allowed : 12.99 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3304 helix: 1.91 (0.20), residues: 650 sheet: 0.48 (0.17), residues: 832 loop : -0.37 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 436 HIS 0.007 0.002 HIS B 519 PHE 0.021 0.002 PHE C 86 TYR 0.019 0.002 TYR B1067 ARG 0.005 0.001 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 253 time to evaluate : 3.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8138 (m-80) cc_final: 0.7828 (m-80) REVERT: A 133 PHE cc_start: 0.7072 (m-80) cc_final: 0.6094 (t80) REVERT: A 136 CYS cc_start: 0.6374 (m) cc_final: 0.6126 (t) REVERT: A 137 ASN cc_start: 0.6918 (m-40) cc_final: 0.6488 (p0) REVERT: A 169 GLU cc_start: 0.8618 (tt0) cc_final: 0.8243 (tm-30) REVERT: A 200 TYR cc_start: 0.6511 (p90) cc_final: 0.5382 (p90) REVERT: A 228 ASP cc_start: 0.8851 (m-30) cc_final: 0.8450 (m-30) REVERT: A 309 GLU cc_start: 0.8351 (pm20) cc_final: 0.7768 (mt-10) REVERT: A 316 SER cc_start: 0.9291 (t) cc_final: 0.9040 (p) REVERT: A 343 ASN cc_start: 0.5667 (m-40) cc_final: 0.4799 (t0) REVERT: A 697 MET cc_start: 0.9039 (ptm) cc_final: 0.8474 (ptm) REVERT: A 735 SER cc_start: 0.8974 (t) cc_final: 0.8595 (p) REVERT: A 1113 GLN cc_start: 0.9052 (mm110) cc_final: 0.8671 (mt0) REVERT: B 41 LYS cc_start: 0.7122 (pttt) cc_final: 0.6859 (ptpp) REVERT: B 554 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8323 (pp20) REVERT: B 616 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.7227 (m110) REVERT: B 675 GLN cc_start: 0.8145 (mt0) cc_final: 0.7575 (pp30) REVERT: B 745 ASP cc_start: 0.8085 (m-30) cc_final: 0.7732 (p0) REVERT: B 1050 MET cc_start: 0.9166 (ptm) cc_final: 0.8934 (ptm) REVERT: B 1073 LYS cc_start: 0.8718 (mttt) cc_final: 0.8256 (mptt) REVERT: B 1092 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8629 (pt0) REVERT: B 1106 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.8934 (pt0) REVERT: C 191 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8200 (mm-30) REVERT: C 239 GLN cc_start: 0.8186 (pt0) cc_final: 0.7595 (mt0) REVERT: C 359 SER cc_start: 0.8292 (p) cc_final: 0.7960 (m) REVERT: C 360 ASN cc_start: 0.8572 (t0) cc_final: 0.8247 (m-40) REVERT: C 378 LYS cc_start: 0.7462 (tttt) cc_final: 0.7138 (mmmt) REVERT: C 380 TYR cc_start: 0.8469 (m-80) cc_final: 0.8268 (m-80) REVERT: C 388 ASN cc_start: 0.8210 (m110) cc_final: 0.7993 (t0) REVERT: C 565 PHE cc_start: 0.7313 (p90) cc_final: 0.7071 (p90) REVERT: C 646 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8359 (tpt-90) REVERT: C 675 GLN cc_start: 0.8440 (mt0) cc_final: 0.7502 (pp30) REVERT: C 868 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8486 (mp0) REVERT: C 869 MET cc_start: 0.9159 (mtt) cc_final: 0.8898 (mtp) REVERT: C 950 ASP cc_start: 0.8807 (t70) cc_final: 0.8322 (m-30) REVERT: C 960 ASN cc_start: 0.8440 (m-40) cc_final: 0.8095 (t0) REVERT: C 985 ASP cc_start: 0.7773 (m-30) cc_final: 0.7236 (p0) REVERT: C 1045 LYS cc_start: 0.9099 (mttt) cc_final: 0.8444 (ttpp) REVERT: C 1081 ILE cc_start: 0.8936 (pt) cc_final: 0.8591 (mt) REVERT: X 34 MET cc_start: 0.1068 (ptp) cc_final: -0.0282 (tpp) REVERT: Y 12 MET cc_start: 0.1921 (mmt) cc_final: 0.1473 (tpp) REVERT: Y 103 ARG cc_start: 0.7368 (mmm160) cc_final: 0.6821 (mmm160) REVERT: Z 34 MET cc_start: 0.0851 (mmm) cc_final: 0.0515 (ptp) outliers start: 52 outliers final: 41 residues processed: 292 average time/residue: 0.3759 time to fit residues: 177.2138 Evaluate side-chains 291 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 198 optimal weight: 10.0000 chunk 128 optimal weight: 0.0970 chunk 191 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 204 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 GLN A 779 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 207 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27742 Z= 0.157 Angle : 0.499 8.577 37718 Z= 0.256 Chirality : 0.043 0.411 4456 Planarity : 0.003 0.038 4782 Dihedral : 4.847 53.463 4996 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.06 % Favored : 97.91 % Rotamer: Outliers : 1.51 % Allowed : 13.43 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3304 helix: 2.22 (0.20), residues: 653 sheet: 0.54 (0.17), residues: 845 loop : -0.26 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 PHE 0.017 0.001 PHE B 32 TYR 0.018 0.001 TYR B 200 ARG 0.005 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 269 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8115 (m-80) cc_final: 0.7826 (m-80) REVERT: A 133 PHE cc_start: 0.6772 (m-80) cc_final: 0.5708 (t80) REVERT: A 136 CYS cc_start: 0.6473 (m) cc_final: 0.6202 (t) REVERT: A 137 ASN cc_start: 0.6893 (m-40) cc_final: 0.6413 (p0) REVERT: A 169 GLU cc_start: 0.8607 (tt0) cc_final: 0.8251 (tm-30) REVERT: A 200 TYR cc_start: 0.6476 (p90) cc_final: 0.5363 (p90) REVERT: A 228 ASP cc_start: 0.8815 (m-30) cc_final: 0.8424 (m-30) REVERT: A 309 GLU cc_start: 0.8331 (pm20) cc_final: 0.7757 (mt-10) REVERT: A 316 SER cc_start: 0.9296 (t) cc_final: 0.9078 (p) REVERT: A 343 ASN cc_start: 0.5684 (m-40) cc_final: 0.5059 (t0) REVERT: A 697 MET cc_start: 0.9025 (ptm) cc_final: 0.8494 (ptm) REVERT: A 735 SER cc_start: 0.8966 (t) cc_final: 0.8602 (p) REVERT: A 779 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8447 (tp40) REVERT: A 854 LYS cc_start: 0.5322 (tmtt) cc_final: 0.4216 (ptpt) REVERT: A 1113 GLN cc_start: 0.9003 (mm110) cc_final: 0.8715 (mt0) REVERT: B 41 LYS cc_start: 0.6899 (pttt) cc_final: 0.6633 (ptpp) REVERT: B 106 PHE cc_start: 0.6873 (m-80) cc_final: 0.6582 (m-80) REVERT: B 117 LEU cc_start: 0.7609 (tp) cc_final: 0.6855 (mp) REVERT: B 287 ASP cc_start: 0.8617 (t0) cc_final: 0.8110 (m-30) REVERT: B 378 LYS cc_start: 0.7822 (tttt) cc_final: 0.7354 (mmtp) REVERT: B 380 TYR cc_start: 0.8141 (m-10) cc_final: 0.7724 (m-80) REVERT: B 403 ARG cc_start: 0.6762 (ptt-90) cc_final: 0.6238 (ptt-90) REVERT: B 554 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8281 (pp20) REVERT: B 616 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.7147 (m110) REVERT: B 675 GLN cc_start: 0.8078 (mt0) cc_final: 0.7532 (pp30) REVERT: B 745 ASP cc_start: 0.8210 (m-30) cc_final: 0.7861 (p0) REVERT: B 936 ASP cc_start: 0.7918 (m-30) cc_final: 0.7705 (m-30) REVERT: B 985 ASP cc_start: 0.7748 (m-30) cc_final: 0.7101 (p0) REVERT: B 1073 LYS cc_start: 0.8654 (mttt) cc_final: 0.8182 (mptt) REVERT: B 1092 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8583 (pt0) REVERT: C 238 PHE cc_start: 0.7507 (p90) cc_final: 0.7026 (p90) REVERT: C 239 GLN cc_start: 0.8277 (pt0) cc_final: 0.7624 (mt0) REVERT: C 269 TYR cc_start: 0.7858 (m-80) cc_final: 0.7631 (m-80) REVERT: C 305 SER cc_start: 0.9298 (t) cc_final: 0.9008 (p) REVERT: C 351 TYR cc_start: 0.6204 (p90) cc_final: 0.5904 (p90) REVERT: C 359 SER cc_start: 0.8286 (p) cc_final: 0.7955 (m) REVERT: C 360 ASN cc_start: 0.8531 (t0) cc_final: 0.8230 (m-40) REVERT: C 377 PHE cc_start: 0.7525 (t80) cc_final: 0.7140 (t80) REVERT: C 378 LYS cc_start: 0.7445 (tttt) cc_final: 0.7132 (mmmt) REVERT: C 388 ASN cc_start: 0.8199 (m110) cc_final: 0.7989 (t0) REVERT: C 532 ASN cc_start: 0.8492 (t0) cc_final: 0.7776 (m-40) REVERT: C 565 PHE cc_start: 0.7264 (p90) cc_final: 0.6954 (p90) REVERT: C 646 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8435 (tpt-90) REVERT: C 675 GLN cc_start: 0.8416 (mt0) cc_final: 0.7485 (pp30) REVERT: C 868 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8412 (mp0) REVERT: C 869 MET cc_start: 0.9215 (mtt) cc_final: 0.8836 (mtp) REVERT: C 950 ASP cc_start: 0.8689 (t70) cc_final: 0.8186 (m-30) REVERT: C 960 ASN cc_start: 0.8344 (m-40) cc_final: 0.8095 (t0) REVERT: C 985 ASP cc_start: 0.7744 (m-30) cc_final: 0.7205 (p0) REVERT: C 1010 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8215 (pt0) REVERT: C 1045 LYS cc_start: 0.8993 (mttt) cc_final: 0.8587 (tptt) REVERT: C 1081 ILE cc_start: 0.8815 (pt) cc_final: 0.8567 (mt) REVERT: X 34 MET cc_start: 0.1036 (ptp) cc_final: -0.0601 (tpp) REVERT: Y 12 MET cc_start: 0.2058 (mmt) cc_final: 0.1606 (tpp) REVERT: Y 103 ARG cc_start: 0.7378 (mmm160) cc_final: 0.6814 (mmm160) REVERT: Z 34 MET cc_start: 0.0829 (mmm) cc_final: 0.0517 (ptp) outliers start: 44 outliers final: 34 residues processed: 295 average time/residue: 0.3852 time to fit residues: 183.0643 Evaluate side-chains 290 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 291 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 299 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 270 optimal weight: 3.9990 chunk 282 optimal weight: 0.5980 chunk 298 optimal weight: 7.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 27742 Z= 0.160 Angle : 0.500 17.196 37718 Z= 0.254 Chirality : 0.043 0.348 4456 Planarity : 0.003 0.040 4782 Dihedral : 4.649 54.062 4996 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % Rotamer: Outliers : 1.34 % Allowed : 13.57 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3304 helix: 2.26 (0.20), residues: 659 sheet: 0.56 (0.17), residues: 842 loop : -0.25 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 PHE 0.018 0.001 PHE C 643 TYR 0.017 0.001 TYR C1067 ARG 0.005 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 264 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8103 (m-80) cc_final: 0.7767 (m-80) REVERT: A 133 PHE cc_start: 0.6804 (m-80) cc_final: 0.5734 (t80) REVERT: A 136 CYS cc_start: 0.6572 (m) cc_final: 0.6336 (t) REVERT: A 137 ASN cc_start: 0.6935 (m-40) cc_final: 0.6417 (p0) REVERT: A 169 GLU cc_start: 0.8593 (tt0) cc_final: 0.8190 (tm-30) REVERT: A 200 TYR cc_start: 0.6579 (p90) cc_final: 0.5509 (p90) REVERT: A 228 ASP cc_start: 0.8785 (m-30) cc_final: 0.8395 (m-30) REVERT: A 309 GLU cc_start: 0.8355 (pm20) cc_final: 0.7754 (mt-10) REVERT: A 316 SER cc_start: 0.9307 (t) cc_final: 0.9085 (p) REVERT: A 343 ASN cc_start: 0.5374 (m-40) cc_final: 0.4787 (t0) REVERT: A 697 MET cc_start: 0.9022 (ptm) cc_final: 0.8494 (ptm) REVERT: A 735 SER cc_start: 0.8978 (t) cc_final: 0.8619 (p) REVERT: A 854 LYS cc_start: 0.5319 (tmtt) cc_final: 0.4257 (ptpt) REVERT: A 1113 GLN cc_start: 0.8947 (mm110) cc_final: 0.8692 (mt0) REVERT: B 41 LYS cc_start: 0.6993 (pttt) cc_final: 0.6740 (ptpp) REVERT: B 53 ASP cc_start: 0.8118 (t0) cc_final: 0.7881 (t0) REVERT: B 106 PHE cc_start: 0.6935 (m-80) cc_final: 0.6647 (m-80) REVERT: B 117 LEU cc_start: 0.7579 (tp) cc_final: 0.6795 (mp) REVERT: B 378 LYS cc_start: 0.7828 (tttt) cc_final: 0.7612 (mmtp) REVERT: B 403 ARG cc_start: 0.6764 (ptt-90) cc_final: 0.6234 (ptt-90) REVERT: B 554 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8250 (pp20) REVERT: B 675 GLN cc_start: 0.8067 (mt0) cc_final: 0.7520 (pp30) REVERT: B 745 ASP cc_start: 0.8228 (m-30) cc_final: 0.7868 (p0) REVERT: B 936 ASP cc_start: 0.7913 (m-30) cc_final: 0.7699 (m-30) REVERT: B 1050 MET cc_start: 0.9091 (ptm) cc_final: 0.8878 (ptm) REVERT: B 1073 LYS cc_start: 0.8657 (mttt) cc_final: 0.8173 (mptt) REVERT: B 1092 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8581 (pt0) REVERT: C 238 PHE cc_start: 0.7455 (p90) cc_final: 0.6995 (p90) REVERT: C 239 GLN cc_start: 0.8296 (pt0) cc_final: 0.7643 (mt0) REVERT: C 269 TYR cc_start: 0.7803 (m-80) cc_final: 0.7542 (m-80) REVERT: C 305 SER cc_start: 0.9280 (t) cc_final: 0.9008 (p) REVERT: C 351 TYR cc_start: 0.6217 (p90) cc_final: 0.5923 (p90) REVERT: C 359 SER cc_start: 0.8233 (p) cc_final: 0.7905 (m) REVERT: C 360 ASN cc_start: 0.8547 (t0) cc_final: 0.8237 (m-40) REVERT: C 377 PHE cc_start: 0.7501 (t80) cc_final: 0.7124 (t80) REVERT: C 378 LYS cc_start: 0.7479 (tttt) cc_final: 0.7146 (mmmt) REVERT: C 388 ASN cc_start: 0.8211 (m110) cc_final: 0.8006 (t0) REVERT: C 532 ASN cc_start: 0.8492 (t0) cc_final: 0.7790 (m-40) REVERT: C 537 LYS cc_start: 0.8271 (mttt) cc_final: 0.7743 (mmtm) REVERT: C 565 PHE cc_start: 0.7236 (p90) cc_final: 0.6923 (p90) REVERT: C 646 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8385 (tpt-90) REVERT: C 675 GLN cc_start: 0.8404 (mt0) cc_final: 0.7467 (pp30) REVERT: C 868 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8410 (mp0) REVERT: C 869 MET cc_start: 0.9213 (mtt) cc_final: 0.8827 (mtp) REVERT: C 950 ASP cc_start: 0.8672 (t70) cc_final: 0.8163 (m-30) REVERT: C 960 ASN cc_start: 0.8327 (m-40) cc_final: 0.8086 (t0) REVERT: C 985 ASP cc_start: 0.7607 (m-30) cc_final: 0.7037 (p0) REVERT: C 1045 LYS cc_start: 0.8987 (mttt) cc_final: 0.8366 (ttpp) REVERT: C 1081 ILE cc_start: 0.8804 (pt) cc_final: 0.8578 (mt) REVERT: X 34 MET cc_start: 0.1032 (ptp) cc_final: -0.0537 (tpp) REVERT: Y 12 MET cc_start: 0.2164 (mmt) cc_final: 0.1703 (tpp) REVERT: Y 103 ARG cc_start: 0.7383 (mmm160) cc_final: 0.6819 (mmm160) REVERT: Z 34 MET cc_start: 0.0872 (mmm) cc_final: 0.0477 (ptp) outliers start: 39 outliers final: 35 residues processed: 287 average time/residue: 0.3900 time to fit residues: 179.6752 Evaluate side-chains 288 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 196 optimal weight: 1.9990 chunk 316 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 219 optimal weight: 0.0770 chunk 331 optimal weight: 10.0000 chunk 305 optimal weight: 50.0000 chunk 264 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 334 ASN A 613 GLN A 779 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS X 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27742 Z= 0.239 Angle : 0.523 14.977 37718 Z= 0.266 Chirality : 0.043 0.292 4456 Planarity : 0.003 0.041 4782 Dihedral : 4.697 53.408 4996 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.48 % Allowed : 13.47 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3304 helix: 2.19 (0.20), residues: 659 sheet: 0.55 (0.17), residues: 849 loop : -0.30 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 PHE 0.018 0.001 PHE C 643 TYR 0.017 0.001 TYR B1067 ARG 0.004 0.000 ARG B 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 256 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8104 (m-80) cc_final: 0.7756 (m-80) REVERT: A 133 PHE cc_start: 0.6913 (m-80) cc_final: 0.5794 (t80) REVERT: A 136 CYS cc_start: 0.6601 (m) cc_final: 0.6358 (t) REVERT: A 137 ASN cc_start: 0.6867 (m-40) cc_final: 0.6364 (p0) REVERT: A 169 GLU cc_start: 0.8628 (tt0) cc_final: 0.8254 (tm-30) REVERT: A 200 TYR cc_start: 0.6701 (p90) cc_final: 0.5685 (p90) REVERT: A 228 ASP cc_start: 0.8805 (m-30) cc_final: 0.8595 (m-30) REVERT: A 309 GLU cc_start: 0.8367 (pm20) cc_final: 0.7780 (mt-10) REVERT: A 316 SER cc_start: 0.9310 (t) cc_final: 0.9089 (p) REVERT: A 326 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6633 (tt) REVERT: A 343 ASN cc_start: 0.5715 (m-40) cc_final: 0.5141 (t0) REVERT: A 697 MET cc_start: 0.9029 (ptm) cc_final: 0.8504 (ptm) REVERT: A 735 SER cc_start: 0.8958 (t) cc_final: 0.8582 (p) REVERT: A 854 LYS cc_start: 0.5384 (tmtt) cc_final: 0.4318 (ptpt) REVERT: A 1113 GLN cc_start: 0.8980 (mm110) cc_final: 0.8679 (mt0) REVERT: B 41 LYS cc_start: 0.7029 (pttt) cc_final: 0.6776 (ptpp) REVERT: B 53 ASP cc_start: 0.8125 (t0) cc_final: 0.7886 (t0) REVERT: B 117 LEU cc_start: 0.7624 (tp) cc_final: 0.6885 (mp) REVERT: B 287 ASP cc_start: 0.8614 (t0) cc_final: 0.8125 (m-30) REVERT: B 378 LYS cc_start: 0.7866 (tttt) cc_final: 0.7563 (mmtp) REVERT: B 380 TYR cc_start: 0.8019 (m-10) cc_final: 0.7751 (m-10) REVERT: B 403 ARG cc_start: 0.6926 (ptt-90) cc_final: 0.6588 (ptt-90) REVERT: B 554 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8256 (pp20) REVERT: B 616 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.7174 (m110) REVERT: B 675 GLN cc_start: 0.8063 (mt0) cc_final: 0.7518 (pp30) REVERT: B 745 ASP cc_start: 0.8251 (m-30) cc_final: 0.7879 (p0) REVERT: B 1050 MET cc_start: 0.9136 (ptm) cc_final: 0.8914 (ptm) REVERT: B 1073 LYS cc_start: 0.8706 (mttt) cc_final: 0.8221 (mptt) REVERT: B 1092 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8566 (pt0) REVERT: C 191 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8316 (mm-30) REVERT: C 238 PHE cc_start: 0.7319 (p90) cc_final: 0.6971 (p90) REVERT: C 239 GLN cc_start: 0.8291 (pt0) cc_final: 0.7627 (mt0) REVERT: C 269 TYR cc_start: 0.7747 (m-80) cc_final: 0.7473 (m-80) REVERT: C 305 SER cc_start: 0.9281 (t) cc_final: 0.8963 (p) REVERT: C 351 TYR cc_start: 0.6330 (p90) cc_final: 0.6019 (p90) REVERT: C 359 SER cc_start: 0.8246 (p) cc_final: 0.7919 (m) REVERT: C 360 ASN cc_start: 0.8555 (t0) cc_final: 0.8240 (m-40) REVERT: C 377 PHE cc_start: 0.7590 (t80) cc_final: 0.7233 (t80) REVERT: C 378 LYS cc_start: 0.7520 (tttt) cc_final: 0.7192 (mmmt) REVERT: C 388 ASN cc_start: 0.8246 (m110) cc_final: 0.7698 (t0) REVERT: C 532 ASN cc_start: 0.8489 (t0) cc_final: 0.7790 (m-40) REVERT: C 537 LYS cc_start: 0.8279 (mttt) cc_final: 0.7754 (mmtm) REVERT: C 565 PHE cc_start: 0.7257 (p90) cc_final: 0.6965 (p90) REVERT: C 646 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8366 (tpt-90) REVERT: C 675 GLN cc_start: 0.8408 (mt0) cc_final: 0.7450 (pp30) REVERT: C 868 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8475 (mp0) REVERT: C 869 MET cc_start: 0.9182 (mtt) cc_final: 0.8735 (mtp) REVERT: C 950 ASP cc_start: 0.8730 (t70) cc_final: 0.8212 (m-30) REVERT: C 960 ASN cc_start: 0.8381 (m-40) cc_final: 0.8078 (t0) REVERT: C 985 ASP cc_start: 0.7667 (m-30) cc_final: 0.7083 (p0) REVERT: C 1045 LYS cc_start: 0.9051 (mttt) cc_final: 0.8416 (ttpp) REVERT: C 1081 ILE cc_start: 0.8853 (pt) cc_final: 0.8590 (mt) REVERT: X 34 MET cc_start: 0.1053 (ptp) cc_final: -0.0557 (tpp) REVERT: Y 12 MET cc_start: 0.2290 (mmt) cc_final: 0.1838 (tpp) REVERT: Y 103 ARG cc_start: 0.7350 (mmm160) cc_final: 0.6791 (mmm160) REVERT: Z 34 MET cc_start: 0.0953 (mmm) cc_final: 0.0576 (ptp) outliers start: 43 outliers final: 34 residues processed: 283 average time/residue: 0.4001 time to fit residues: 181.1018 Evaluate side-chains 285 residues out of total 2911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 248 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 209 optimal weight: 9.9990 chunk 281 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 264 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 271 optimal weight: 0.0870 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 GLN A 779 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.193811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.148846 restraints weight = 32839.769| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.13 r_work: 0.3294 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27742 Z= 0.215 Angle : 0.512 14.246 37718 Z= 0.260 Chirality : 0.043 0.290 4456 Planarity : 0.003 0.041 4782 Dihedral : 4.637 53.418 4996 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 1.24 % Allowed : 13.88 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3304 helix: 2.21 (0.20), residues: 659 sheet: 0.58 (0.17), residues: 847 loop : -0.28 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.018 0.001 PHE C 643 TYR 0.017 0.001 TYR B1067 ARG 0.004 0.000 ARG B 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5699.95 seconds wall clock time: 104 minutes 44.39 seconds (6284.39 seconds total)