Starting phenix.real_space_refine on Mon Feb 19 12:47:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edg_31070/02_2024/7edg_31070.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edg_31070/02_2024/7edg_31070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edg_31070/02_2024/7edg_31070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edg_31070/02_2024/7edg_31070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edg_31070/02_2024/7edg_31070.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edg_31070/02_2024/7edg_31070.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 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 108 5.16 5 C 15724 2.51 5 N 3999 2.21 5 O 4884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 136": "OD1" <-> "OD2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A GLU 987": "OE1" <-> "OE2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 805": "OD1" <-> "OD2" Residue "B TYR 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1069": "OE1" <-> "OE2" Residue "C PHE 1072": "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: 24715 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 7922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7922 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 51, 'TRANS': 963} Chain breaks: 7 Chain: "B" Number of atoms: 7811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7811 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 49, 'TRANS': 950} Chain breaks: 8 Chain: "C" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7879 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 50, 'TRANS': 957} Chain breaks: 8 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 12.91, per 1000 atoms: 0.52 Number of scatterers: 24715 At special positions: 0 Unit cell: (133.1, 141.9, 198, 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 108 16.00 O 4884 8.00 N 3999 7.00 C 15724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " distance=2.04 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " 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 E 2 " - " BMA E 3 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 162 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 120 " " NAG B2003 " - " ASN B 162 " " NAG B2004 " - " ASN B 231 " " NAG B2005 " - " ASN B 328 " " NAG B2006 " - " ASN B 600 " " NAG B2007 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 120 " " NAG C2003 " - " ASN C 162 " " NAG C2004 " - " ASN C 231 " " NAG C2005 " - " ASN C 328 " " NAG C2006 " - " ASN C 600 " " NAG C2007 " - " ASN C 654 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 231 " " NAG F 1 " - " ASN A 279 " " NAG G 1 " - " ASN A 328 " " NAG H 1 " - " ASN A 340 " " NAG I 1 " - " ASN A 613 " " NAG J 1 " - " ASN A 706 " " NAG K 1 " - " ASN A 714 " " NAG L 1 " - " ASN A 798 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN A1095 " " NAG O 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN B 340 " " NAG R 1 " - " ASN B 613 " " NAG S 1 " - " ASN B 706 " " NAG T 1 " - " ASN B 714 " " NAG U 1 " - " ASN B 798 " " NAG V 1 " - " ASN B1071 " " NAG W 1 " - " ASN B1095 " " NAG X 1 " - " ASN B1131 " " NAG Y 1 " - " ASN C 279 " " NAG Z 1 " - " ASN C 340 " " NAG a 1 " - " ASN C 613 " " NAG b 1 " - " ASN C 706 " " NAG c 1 " - " ASN C 714 " " NAG d 1 " - " ASN C 798 " " NAG e 1 " - " ASN C1071 " " NAG f 1 " - " ASN C1095 " " NAG g 1 " - " ASN C1131 " Time building additional restraints: 10.54 Conformation dependent library (CDL) restraints added in 4.2 seconds 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5662 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 42 sheets defined 24.3% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.818A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.661A pdb=" N GLN A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 543 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.655A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.768A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 822 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 910 through 915 removed outlier: 3.784A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 915' Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.659A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 942 removed outlier: 3.988A pdb=" N LEU A 942 " --> pdb=" O ALA A 939 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 939 through 942' Processing helix chain 'A' and resid 946 through 962 Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.650A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.975A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1030 removed outlier: 3.521A pdb=" N ARG A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 removed outlier: 4.415A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.951A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.296A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.510A pdb=" N TYR B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 757 through 780 removed outlier: 3.660A pdb=" N PHE B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.514A pdb=" N ASN B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.532A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.627A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 907 No H-bonds generated for 'chain 'B' and resid 905 through 907' Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.701A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.723A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 3.533A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.514A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.452A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 3.940A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B1143 " --> pdb=" O GLN B1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.585A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 382 through 386 removed outlier: 4.139A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 382 through 386' Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.524A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.546A pdb=" N TYR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.821A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 762 " --> pdb=" O THR C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 822 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.586A pdb=" N ILE C 867 " --> pdb=" O THR C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.604A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.694A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 915 removed outlier: 3.977A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 910 through 915' Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 removed outlier: 3.587A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.527A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.827A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.794A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 188 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 190 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 199 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N HIS A 204 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N LEU A 220 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.022A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN C 537 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.724A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.522A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.082A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.138A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.534A pdb=" N TYR A 470 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 562 through 563 removed outlier: 7.402A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.965A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.983A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.591A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.564A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 731 through 732 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.677A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 264 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE B 200 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL B 224 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.839A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.729A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.624A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.051A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC7, first strand: chain 'B' and resid 562 through 563 removed outlier: 3.845A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.242A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 698 through 701 removed outlier: 6.551A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LYS C 787 " --> pdb=" O ALA B 698 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASN B 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 714 through 725 removed outlier: 3.607A pdb=" N GLY B1056 " --> pdb=" O ALA B1053 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.521A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1073 through 1075 removed outlier: 4.004A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.587A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.751A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.721A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.607A pdb=" N SER C 169 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 316 removed outlier: 7.034A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE1, first strand: chain 'C' and resid 388 through 389 removed outlier: 3.670A pdb=" N VAL C 521 " --> pdb=" O PHE C 389 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.935A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 708 through 725 removed outlier: 7.021A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 708 through 725 removed outlier: 7.021A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.613A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1117 through 1119 removed outlier: 3.670A pdb=" N CYS C1079 " --> pdb=" O VAL C1130 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2307 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: 9.78 Time building geometry restraints manager: 11.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7757 1.34 - 1.46: 6279 1.46 - 1.59: 11080 1.59 - 1.71: 1 1.71 - 1.83: 132 Bond restraints: 25249 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" N LYS B 851 " pdb=" CA LYS B 851 " ideal model delta sigma weight residual 1.461 1.428 0.033 1.47e-02 4.63e+03 4.98e+00 bond pdb=" CB PRO C 496 " pdb=" CG PRO C 496 " ideal model delta sigma weight residual 1.492 1.587 -0.095 5.00e-02 4.00e+02 3.64e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 ... (remaining 25244 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.56: 645 106.56 - 114.03: 14746 114.03 - 121.50: 12613 121.50 - 128.97: 6262 128.97 - 136.44: 80 Bond angle restraints: 34346 Sorted by residual: angle pdb=" N LYS B 851 " pdb=" CA LYS B 851 " pdb=" C LYS B 851 " ideal model delta sigma weight residual 108.54 119.93 -11.39 1.41e+00 5.03e-01 6.52e+01 angle pdb=" C THR C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.84 127.91 -8.07 1.25e+00 6.40e-01 4.16e+01 angle pdb=" N THR C 205 " pdb=" CA THR C 205 " pdb=" C THR C 205 " ideal model delta sigma weight residual 109.81 122.72 -12.91 2.21e+00 2.05e-01 3.41e+01 angle pdb=" N VAL A 128 " pdb=" CA VAL A 128 " pdb=" C VAL A 128 " ideal model delta sigma weight residual 111.77 105.78 5.99 1.04e+00 9.25e-01 3.31e+01 angle pdb=" C GLU A 94 " pdb=" CA GLU A 94 " pdb=" CB GLU A 94 " ideal model delta sigma weight residual 116.54 110.08 6.46 1.15e+00 7.56e-01 3.15e+01 ... (remaining 34341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.67: 14970 22.67 - 45.34: 874 45.34 - 68.00: 136 68.00 - 90.67: 41 90.67 - 113.34: 23 Dihedral angle restraints: 16044 sinusoidal: 7250 harmonic: 8794 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual 93.00 -179.83 -87.17 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual -86.00 -172.82 86.82 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS B 659 " pdb=" SG CYS B 659 " pdb=" SG CYS B 668 " pdb=" CB CYS B 668 " ideal model delta sinusoidal sigma weight residual 93.00 176.82 -83.82 1 1.00e+01 1.00e-02 8.57e+01 ... (remaining 16041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4054 0.116 - 0.233: 70 0.233 - 0.349: 8 0.349 - 0.465: 2 0.465 - 0.581: 1 Chirality restraints: 4135 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 340 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C1 NAG B2002 " pdb=" ND2 ASN B 120 " pdb=" C2 NAG B2002 " pdb=" O5 NAG B2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 4132 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 408 " -0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO A 409 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 205 " -0.056 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO C 206 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 495 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO C 496 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 496 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 496 " -0.042 5.00e-02 4.00e+02 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 2 2.07 - 2.78: 4946 2.78 - 3.48: 31737 3.48 - 4.19: 51599 4.19 - 4.90: 93286 Nonbonded interactions: 181570 Sorted by model distance: nonbonded pdb=" CA ASN C 185 " pdb=" CG2 THR C 205 " model vdw 1.362 3.890 nonbonded pdb=" CB ASN C 185 " pdb=" CG2 THR C 205 " model vdw 1.686 3.860 nonbonded pdb=" CB ASN C 185 " pdb=" OG1 THR C 205 " model vdw 2.079 3.440 nonbonded pdb=" O LEU C 186 " pdb=" O HIS C 204 " model vdw 2.156 3.040 nonbonded pdb=" O PHE B 131 " pdb=" OG SER B 158 " model vdw 2.164 2.440 ... (remaining 181565 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 138 or resid 159 through 170 or resid 184 throu \ gh 206 or resid 215 through 240 or resid 262 through 617 or resid 638 through 67 \ 2 or resid 688 through 1143 or resid 2001 through 2004)) selection = (chain 'B' and (resid 27 through 138 or resid 159 through 170 or resid 184 throu \ gh 617 or resid 638 through 824 or resid 846 through 1143 or resid 2002 through \ 2005)) selection = (chain 'C' and (resid 27 through 138 or resid 158 or resid 160 through 170 or re \ sid 184 through 206 or resid 215 through 260 or resid 262 through 841 or resid 8 \ 48 through 1143 or resid 2002 through 2005)) } ncs_group { reference = chain 'D' 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' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 13.690 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 66.480 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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 : 0.004 0.095 25249 Z= 0.274 Angle : 0.679 12.907 34346 Z= 0.351 Chirality : 0.050 0.581 4135 Planarity : 0.005 0.090 4336 Dihedral : 14.761 113.340 10277 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.73 % Favored : 92.90 % Rotamer: Outliers : 0.45 % Allowed : 0.34 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2971 helix: 1.36 (0.23), residues: 622 sheet: 0.06 (0.20), residues: 663 loop : -1.88 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 64 HIS 0.004 0.001 HIS C1080 PHE 0.028 0.001 PHE A 903 TYR 0.015 0.001 TYR A1064 ARG 0.005 0.000 ARG B1104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 2.550 Fit side-chains revert: symmetry clash REVERT: A 187 ARG cc_start: 0.7293 (mtt-85) cc_final: 0.7021 (mtt-85) REVERT: B 28 TYR cc_start: 0.6854 (m-10) cc_final: 0.6625 (m-10) REVERT: C 348 TYR cc_start: 0.8411 (p90) cc_final: 0.8125 (p90) REVERT: C 505 TYR cc_start: 0.7734 (m-80) cc_final: 0.7408 (m-80) outliers start: 12 outliers final: 1 residues processed: 165 average time/residue: 0.3356 time to fit residues: 91.3118 Evaluate side-chains 115 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 0.0370 chunk 228 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 77 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 273 optimal weight: 0.0010 overall best weight: 1.1268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 484 ASN B 999 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25249 Z= 0.235 Angle : 0.595 11.320 34346 Z= 0.299 Chirality : 0.047 0.439 4135 Planarity : 0.004 0.106 4336 Dihedral : 9.750 97.303 4889 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.66 % Favored : 93.07 % Rotamer: Outliers : 0.87 % Allowed : 6.22 % Favored : 92.91 % 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: -0.91 (0.16), residues: 2971 helix: 1.47 (0.22), residues: 659 sheet: -0.00 (0.19), residues: 705 loop : -1.88 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 64 HIS 0.007 0.001 HIS C 204 PHE 0.021 0.001 PHE A1118 TYR 0.017 0.001 TYR C 901 ARG 0.003 0.000 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 2.780 Fit side-chains REVERT: C 362 TYR cc_start: 0.8362 (m-80) cc_final: 0.8146 (m-80) REVERT: C 901 TYR cc_start: 0.7116 (m-10) cc_final: 0.6607 (m-10) outliers start: 23 outliers final: 20 residues processed: 140 average time/residue: 0.3104 time to fit residues: 74.3105 Evaluate side-chains 133 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1024 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 227 optimal weight: 0.0870 chunk 186 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 chunk 273 optimal weight: 3.9990 chunk 295 optimal weight: 0.5980 chunk 243 optimal weight: 0.7980 chunk 271 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 25249 Z= 0.149 Angle : 0.544 11.514 34346 Z= 0.271 Chirality : 0.045 0.424 4135 Planarity : 0.004 0.107 4336 Dihedral : 8.845 93.368 4889 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.09 % Favored : 93.64 % Rotamer: Outliers : 1.10 % Allowed : 8.95 % Favored : 89.95 % 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: -0.78 (0.16), residues: 2971 helix: 1.70 (0.22), residues: 659 sheet: 0.07 (0.20), residues: 688 loop : -1.82 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.003 0.000 HIS C 204 PHE 0.012 0.001 PHE A1118 TYR 0.014 0.001 TYR B1064 ARG 0.002 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 2.849 Fit side-chains REVERT: C 268 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.7002 (mt0) REVERT: C 901 TYR cc_start: 0.7219 (m-10) cc_final: 0.6933 (m-10) outliers start: 29 outliers final: 21 residues processed: 142 average time/residue: 0.3279 time to fit residues: 80.3940 Evaluate side-chains 134 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1079 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 270 optimal weight: 2.9990 chunk 205 optimal weight: 0.0020 chunk 142 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 260 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN B 999 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 910 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25249 Z= 0.235 Angle : 0.574 12.034 34346 Z= 0.286 Chirality : 0.046 0.413 4135 Planarity : 0.004 0.111 4336 Dihedral : 8.182 90.225 4887 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.17 % Favored : 92.60 % Rotamer: Outliers : 1.67 % Allowed : 10.65 % Favored : 87.68 % 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: -0.83 (0.16), residues: 2971 helix: 1.57 (0.21), residues: 676 sheet: 0.06 (0.19), residues: 697 loop : -1.87 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 64 HIS 0.004 0.001 HIS C1080 PHE 0.022 0.001 PHE A1118 TYR 0.018 0.001 TYR A1064 ARG 0.002 0.000 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 116 time to evaluate : 2.730 Fit side-chains REVERT: C 268 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7018 (mt0) REVERT: C 348 TYR cc_start: 0.8504 (p90) cc_final: 0.8157 (p90) REVERT: C 901 TYR cc_start: 0.7312 (m-10) cc_final: 0.7111 (m-10) outliers start: 44 outliers final: 35 residues processed: 152 average time/residue: 0.3108 time to fit residues: 82.4582 Evaluate side-chains 148 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 242 optimal weight: 0.0370 chunk 165 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 216 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 73 optimal weight: 0.0370 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN B 999 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25249 Z= 0.166 Angle : 0.537 11.997 34346 Z= 0.268 Chirality : 0.045 0.405 4135 Planarity : 0.004 0.113 4336 Dihedral : 7.503 88.588 4887 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.36 % Favored : 93.40 % Rotamer: Outliers : 1.63 % Allowed : 11.68 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2971 helix: 1.63 (0.22), residues: 672 sheet: 0.08 (0.19), residues: 708 loop : -1.78 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.003 0.001 HIS C1085 PHE 0.015 0.001 PHE A1118 TYR 0.015 0.001 TYR B1064 ARG 0.002 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 119 time to evaluate : 2.794 Fit side-chains REVERT: A 999 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6949 (mp10) REVERT: B 728 MET cc_start: 0.8185 (ptt) cc_final: 0.7979 (ptt) REVERT: C 348 TYR cc_start: 0.8580 (p90) cc_final: 0.8159 (p90) REVERT: C 537 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.7158 (p0) outliers start: 43 outliers final: 31 residues processed: 156 average time/residue: 0.3097 time to fit residues: 84.6356 Evaluate side-chains 148 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 97 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 71 optimal weight: 0.0370 chunk 291 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 134 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 850 GLN B 419 ASN B 910 GLN ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 748 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25249 Z= 0.193 Angle : 0.541 12.019 34346 Z= 0.271 Chirality : 0.045 0.401 4135 Planarity : 0.004 0.116 4336 Dihedral : 7.111 88.096 4887 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.73 % Favored : 93.07 % Rotamer: Outliers : 1.97 % Allowed : 12.47 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.77 (0.16), residues: 2971 helix: 1.56 (0.21), residues: 678 sheet: 0.06 (0.19), residues: 710 loop : -1.80 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.004 0.001 HIS C1085 PHE 0.018 0.001 PHE A1118 TYR 0.019 0.001 TYR C 901 ARG 0.002 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 118 time to evaluate : 2.700 Fit side-chains REVERT: A 550 THR cc_start: 0.7674 (OUTLIER) cc_final: 0.7450 (m) REVERT: A 999 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: B 728 MET cc_start: 0.8206 (ptt) cc_final: 0.8000 (ptt) REVERT: C 505 TYR cc_start: 0.7699 (m-80) cc_final: 0.7366 (m-80) REVERT: C 901 TYR cc_start: 0.7090 (m-10) cc_final: 0.6596 (m-80) outliers start: 52 outliers final: 40 residues processed: 161 average time/residue: 0.2957 time to fit residues: 82.9695 Evaluate side-chains 155 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 113 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 280 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1055 HIS B 119 ASN B 357 ASN ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN C 85 ASN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 25249 Z= 0.364 Angle : 0.631 12.890 34346 Z= 0.320 Chirality : 0.048 0.394 4135 Planarity : 0.005 0.119 4336 Dihedral : 7.145 80.368 4887 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.84 % Favored : 91.96 % Rotamer: Outliers : 2.20 % Allowed : 13.50 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2971 helix: 1.32 (0.21), residues: 686 sheet: -0.14 (0.19), residues: 716 loop : -1.93 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 64 HIS 0.006 0.001 HIS C1085 PHE 0.032 0.002 PHE C1118 TYR 0.021 0.002 TYR A1064 ARG 0.003 0.000 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 119 time to evaluate : 2.783 Fit side-chains REVERT: A 550 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7483 (m) REVERT: A 899 MET cc_start: 0.7678 (tpt) cc_final: 0.7392 (mmt) REVERT: A 999 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: B 640 PHE cc_start: 0.7410 (t80) cc_final: 0.6966 (t80) REVERT: C 505 TYR cc_start: 0.7784 (m-80) cc_final: 0.7543 (m-80) REVERT: C 901 TYR cc_start: 0.7254 (m-10) cc_final: 0.6817 (m-80) outliers start: 58 outliers final: 46 residues processed: 166 average time/residue: 0.3090 time to fit residues: 88.7728 Evaluate side-chains 156 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 108 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 179 optimal weight: 0.9980 chunk 115 optimal weight: 0.0970 chunk 173 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 197 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 228 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 759 GLN ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN C 85 ASN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25249 Z= 0.166 Angle : 0.545 12.044 34346 Z= 0.273 Chirality : 0.044 0.385 4135 Planarity : 0.004 0.120 4336 Dihedral : 6.737 72.355 4887 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.09 % Favored : 93.71 % Rotamer: Outliers : 1.97 % Allowed : 13.95 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.81 (0.16), residues: 2971 helix: 1.51 (0.21), residues: 682 sheet: -0.02 (0.19), residues: 717 loop : -1.81 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.003 0.001 HIS C1085 PHE 0.023 0.001 PHE C 235 TYR 0.016 0.001 TYR B1064 ARG 0.003 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 119 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 550 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7407 (m) REVERT: A 571 ASP cc_start: 0.8410 (t0) cc_final: 0.8085 (t0) REVERT: A 999 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: B 875 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8270 (tt) REVERT: C 560 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7153 (mt0) outliers start: 52 outliers final: 40 residues processed: 162 average time/residue: 0.3121 time to fit residues: 87.9042 Evaluate side-chains 159 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 263 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 253 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 269 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 759 GLN ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN C 85 ASN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25249 Z= 0.248 Angle : 0.577 12.464 34346 Z= 0.289 Chirality : 0.046 0.379 4135 Planarity : 0.004 0.121 4336 Dihedral : 6.573 62.814 4887 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.07 % Favored : 92.73 % Rotamer: Outliers : 2.08 % Allowed : 14.06 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.87 (0.16), residues: 2971 helix: 1.45 (0.21), residues: 682 sheet: -0.05 (0.19), residues: 713 loop : -1.83 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.005 0.001 HIS C1085 PHE 0.024 0.001 PHE C 235 TYR 0.018 0.001 TYR A1064 ARG 0.006 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 113 time to evaluate : 3.002 Fit side-chains REVERT: A 187 ARG cc_start: 0.7119 (mtt-85) cc_final: 0.6564 (mtt-85) REVERT: A 550 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7446 (m) REVERT: A 571 ASP cc_start: 0.8375 (t0) cc_final: 0.8057 (t0) REVERT: A 999 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: B 875 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8251 (tt) REVERT: C 560 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: C 901 TYR cc_start: 0.6754 (m-80) cc_final: 0.6363 (m-80) outliers start: 55 outliers final: 44 residues processed: 159 average time/residue: 0.3008 time to fit residues: 83.7786 Evaluate side-chains 160 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 112 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 177 optimal weight: 0.6980 chunk 285 optimal weight: 0.0870 chunk 174 optimal weight: 0.7980 chunk 135 optimal weight: 0.0670 chunk 198 optimal weight: 0.9990 chunk 299 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 184 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN C 85 ASN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 25249 Z= 0.144 Angle : 0.537 11.695 34346 Z= 0.268 Chirality : 0.044 0.375 4135 Planarity : 0.004 0.121 4336 Dihedral : 6.209 58.566 4887 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.96 % Favored : 93.87 % Rotamer: Outliers : 1.82 % Allowed : 14.37 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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 (0.16), residues: 2971 helix: 1.67 (0.22), residues: 676 sheet: 0.02 (0.19), residues: 689 loop : -1.70 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.003 0.001 HIS A 204 PHE 0.020 0.001 PHE C 235 TYR 0.014 0.001 TYR B1064 ARG 0.007 0.000 ARG C 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 118 time to evaluate : 3.091 Fit side-chains revert: symmetry clash REVERT: A 187 ARG cc_start: 0.7004 (mtt-85) cc_final: 0.6508 (mtt-85) REVERT: A 550 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7484 (m) REVERT: A 571 ASP cc_start: 0.8394 (t0) cc_final: 0.8066 (t0) REVERT: A 999 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6917 (mp10) REVERT: B 875 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8262 (tt) REVERT: C 560 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: C 901 TYR cc_start: 0.6605 (m-80) cc_final: 0.6279 (m-80) outliers start: 48 outliers final: 40 residues processed: 157 average time/residue: 0.3303 time to fit residues: 89.6189 Evaluate side-chains 159 residues out of total 2638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 707 ASN Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 189 optimal weight: 2.9990 chunk 254 optimal weight: 0.1980 chunk 73 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 239 optimal weight: 7.9990 chunk 100 optimal weight: 0.0670 chunk 245 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN C 85 ASN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.164999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.117056 restraints weight = 39795.060| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.36 r_work: 0.3532 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25249 Z= 0.179 Angle : 0.546 11.745 34346 Z= 0.272 Chirality : 0.044 0.367 4135 Planarity : 0.004 0.121 4336 Dihedral : 6.021 57.755 4887 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.46 % Favored : 93.40 % Rotamer: Outliers : 2.01 % Allowed : 14.37 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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 (0.16), residues: 2971 helix: 1.61 (0.22), residues: 683 sheet: 0.07 (0.19), residues: 723 loop : -1.72 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.003 0.001 HIS C1080 PHE 0.022 0.001 PHE C 235 TYR 0.015 0.001 TYR A1064 ARG 0.004 0.000 ARG B 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4319.93 seconds wall clock time: 80 minutes 10.86 seconds (4810.86 seconds total)