Starting phenix.real_space_refine on Mon Feb 19 16:04:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8c_31798/02_2024/7v8c_31798.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8c_31798/02_2024/7v8c_31798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8c_31798/02_2024/7v8c_31798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8c_31798/02_2024/7v8c_31798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8c_31798/02_2024/7v8c_31798.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8c_31798/02_2024/7v8c_31798.pdb" } resolution = 3.4 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= 0.040 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 111 5.16 5 C 16030 2.51 5 N 4088 2.21 5 O 4968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25197 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8016 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 50, 'TRANS': 975} Chain breaks: 7 Chain: "B" Number of atoms: 8072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8072 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 51, 'TRANS': 980} Chain breaks: 7 Chain: "C" Number of atoms: 8059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8059 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 51, 'TRANS': 978} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 12.60, per 1000 atoms: 0.50 Number of scatterers: 25197 At special positions: 0 Unit cell: (141.9, 146.3, 196.9, 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 111 16.00 O 4968 8.00 N 4088 7.00 C 16030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " 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 535 " - pdb=" SG CYS A 587 " 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=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.04 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 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.02 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.02 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.02 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=2.02 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 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2003 " - " ASN A 234 " " NAG A2004 " - " ASN A 600 " " NAG A2005 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 328 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 165 " " NAG C2003 " - " ASN C 328 " " NAG C2004 " - " ASN C 600 " " NAG C2005 " - " ASN C 613 " " NAG C2006 " - " ASN C 654 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 279 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN A 340 " " NAG H 1 " - " ASN A 613 " " NAG I 1 " - " ASN A 706 " " NAG J 1 " - " ASN A 714 " " NAG K 1 " - " ASN A 798 " " NAG L 1 " - " ASN A1071 " " NAG M 1 " - " ASN A1095 " " NAG N 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 706 " " NAG b 1 " - " ASN C 714 " " NAG c 1 " - " ASN C 798 " " NAG d 1 " - " ASN C1071 " " NAG e 1 " - " ASN C1095 " " NAG f 1 " - " ASN C1131 " Time building additional restraints: 10.16 Conformation dependent library (CDL) restraints added in 4.2 seconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 25.1% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 removed outlier: 3.546A pdb=" N GLU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.377A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.190A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.551A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.837A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 895 through 906 removed outlier: 4.441A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.554A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.602A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 980 removed outlier: 3.612A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.629A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.062A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 4.383A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.928A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.809A pdb=" N VAL B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.939A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.636A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.722A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 915 removed outlier: 4.161A pdb=" N TYR B 914 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.615A pdb=" N LEU B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 3.790A pdb=" N ALA B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 3.690A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.617A pdb=" N TRP C 350 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 381 through 387 removed outlier: 3.886A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 387 " --> pdb=" O LEU C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 387' Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.199A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.857A pdb=" N THR C 635 " --> pdb=" O VAL C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.997A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.599A pdb=" N GLN C 771 " --> pdb=" O ILE C 767 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.582A pdb=" N ILE C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 904 removed outlier: 3.823A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 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 981 removed outlier: 3.582A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1030 removed outlier: 4.175A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.554A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.566A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.919A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.852A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.272A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.350A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB1, first strand: chain 'A' and resid 570 through 573 removed outlier: 3.835A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.399A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 714 through 725 removed outlier: 3.600A pdb=" N GLY A1056 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.561A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1083 through 1087 removed outlier: 4.689A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A1120 " --> pdb=" O ALA A1084 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.156A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.855A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.796A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.710A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 325 removed outlier: 3.662A pdb=" N ARG B 325 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC6, first strand: chain 'B' and resid 651 through 657 removed outlier: 4.994A pdb=" N THR B 693 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN B 655 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AC8, first strand: chain 'B' and resid 714 through 716 Processing sheet with id=AC9, first strand: chain 'B' and resid 714 through 716 removed outlier: 5.915A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.445A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 3.612A pdb=" N SER B1120 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B1077 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.907A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.871A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.500A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 308 through 313 removed outlier: 5.673A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 322 through 325 removed outlier: 3.607A pdb=" N ARG C 325 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (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 358 through 359 removed outlier: 6.226A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE3, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.513A pdb=" N TYR C 470 " --> pdb=" O TYR C 486 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 486 " --> pdb=" O TYR C 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 651 through 657 removed outlier: 3.512A pdb=" N ALA C 691 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N THR C 693 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN C 655 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.979A pdb=" N GLN C1068 " --> pdb=" O THR C 713 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C1056 " --> pdb=" O ALA C1053 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 732 through 733 Processing sheet with id=AE7, first strand: chain 'C' and resid 1078 through 1079 Processing sheet with id=AE8, first strand: chain 'C' and resid 1085 through 1087 Processing sheet with id=AE9, first strand: chain 'C' and resid 1091 through 1094 947 hydrogen bonds defined for protein. 2574 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: 10.29 Time building geometry restraints manager: 10.86 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: 7935 1.34 - 1.46: 6418 1.46 - 1.58: 11258 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25749 Sorted by residual: bond pdb=" C ILE A 739 " pdb=" N CYS A 740 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.13e+00 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.293 0.041 2.34e-02 1.83e+03 3.03e+00 bond pdb=" C1 NAG A2001 " pdb=" O5 NAG A2001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 25744 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.37: 399 104.37 - 111.80: 12709 111.80 - 119.24: 8249 119.24 - 126.67: 13427 126.67 - 134.10: 251 Bond angle restraints: 35035 Sorted by residual: angle pdb=" N VAL B 984 " pdb=" CA VAL B 984 " pdb=" C VAL B 984 " ideal model delta sigma weight residual 106.21 109.94 -3.73 1.07e+00 8.73e-01 1.22e+01 angle pdb=" C ASN A 328 " pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 121.97 127.92 -5.95 1.80e+00 3.09e-01 1.09e+01 angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" C ASP B 198 " ideal model delta sigma weight residual 111.17 115.42 -4.25 1.41e+00 5.03e-01 9.10e+00 angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.82 127.00 -4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" CA THR A1114 " pdb=" C THR A1114 " pdb=" N ASP A1115 " ideal model delta sigma weight residual 116.84 121.58 -4.74 1.71e+00 3.42e-01 7.67e+00 ... (remaining 35030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14748 17.90 - 35.81: 1212 35.81 - 53.71: 251 53.71 - 71.61: 51 71.61 - 89.51: 27 Dihedral angle restraints: 16289 sinusoidal: 7301 harmonic: 8988 Sorted by residual: dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 2.73 -88.73 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 5.04 87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual 93.00 -179.41 -87.59 1 1.00e+01 1.00e-02 9.20e+01 ... (remaining 16286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4094 0.110 - 0.220: 98 0.220 - 0.330: 3 0.330 - 0.440: 2 0.440 - 0.550: 2 Chirality restraints: 4199 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B1071 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1 NAG C2003 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C2003 " pdb=" O5 NAG C2003 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 4196 not shown) Planarity restraints: 4468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1071 " 0.030 2.00e-02 2.50e+03 2.81e-02 9.87e+00 pdb=" CG ASN B1071 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B1071 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B1071 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 216 " 0.033 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO C 217 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 217 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 217 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 903 " 0.015 2.00e-02 2.50e+03 1.27e-02 2.83e+00 pdb=" CG PHE C 903 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 903 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 903 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 903 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 903 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 903 " 0.003 2.00e-02 2.50e+03 ... (remaining 4465 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 558 2.66 - 3.22: 24351 3.22 - 3.78: 37474 3.78 - 4.34: 49172 4.34 - 4.90: 81656 Nonbonded interactions: 193211 Sorted by model distance: nonbonded pdb=" OD2 ASP A 575 " pdb=" OG1 THR A 578 " model vdw 2.102 2.440 nonbonded pdb=" O PRO A 230 " pdb=" NH1 ARG C 354 " model vdw 2.109 2.520 nonbonded pdb=" O GLY C 877 " pdb=" OG SER C 881 " model vdw 2.149 2.440 nonbonded pdb=" O GLU A 658 " pdb=" OH TYR A 692 " model vdw 2.149 2.440 nonbonded pdb=" OG1 THR B 615 " pdb=" OE1 GLU B 616 " model vdw 2.169 2.440 ... (remaining 193206 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 14 through 260 or resid 262 through 1143 or resid 2001 thr \ ough 2005)) selection = (chain 'B' and (resid 14 through 260 or resid 262 through 618 or resid 632 throu \ gh 824 or resid 852 through 1143 or resid 2001 through 2005)) selection = (chain 'C' and (resid 14 through 618 or resid 632 through 824 or resid 852 throu \ gh 1143 or resid 2001 through 2005)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' 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' } 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: 3.490 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: 13.320 Check model and map are aligned: 0.440 Set scattering table: 0.230 Process input model: 65.540 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.005 0.047 25749 Z= 0.349 Angle : 0.669 8.293 35035 Z= 0.345 Chirality : 0.048 0.550 4199 Planarity : 0.003 0.051 4424 Dihedral : 13.401 89.514 10389 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.81 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3040 helix: 1.52 (0.21), residues: 685 sheet: -0.14 (0.19), residues: 698 loop : -1.35 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 883 HIS 0.003 0.001 HIS B1061 PHE 0.029 0.002 PHE C 903 TYR 0.021 0.001 TYR C 870 ARG 0.008 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0054 (pmm) cc_final: -0.0187 (pmm) REVERT: A 1026 MET cc_start: 0.8157 (tpp) cc_final: 0.7854 (ttp) REVERT: B 242 HIS cc_start: 0.7469 (t70) cc_final: 0.7085 (t70) REVERT: B 461 PHE cc_start: 0.9130 (m-80) cc_final: 0.8414 (m-10) REVERT: B 737 MET cc_start: 0.8202 (tpt) cc_final: 0.7955 (tpt) REVERT: B 852 PHE cc_start: 0.7695 (m-10) cc_final: 0.7430 (m-10) REVERT: B 983 LYS cc_start: 0.9382 (mmpt) cc_final: 0.9122 (tppt) REVERT: C 462 GLU cc_start: 0.8922 (tp30) cc_final: 0.8068 (tm-30) REVERT: C 1047 MET cc_start: 0.7541 (ptm) cc_final: 0.7138 (ptm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.3355 time to fit residues: 92.0097 Evaluate side-chains 93 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 279 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 GLN C 898 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 25749 Z= 0.305 Angle : 0.617 9.404 35035 Z= 0.315 Chirality : 0.046 0.354 4199 Planarity : 0.004 0.041 4424 Dihedral : 7.419 57.029 4887 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.32 % Favored : 93.52 % Rotamer: Outliers : 0.74 % Allowed : 7.21 % Favored : 92.05 % 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: -0.66 (0.15), residues: 3040 helix: 1.43 (0.21), residues: 680 sheet: -0.05 (0.19), residues: 718 loop : -1.48 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.006 0.001 HIS C1061 PHE 0.029 0.002 PHE A1118 TYR 0.021 0.002 TYR B 420 ARG 0.006 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0149 (pmm) cc_final: -0.0408 (pmm) REVERT: A 335 PHE cc_start: 0.7773 (m-80) cc_final: 0.7356 (m-80) REVERT: A 875 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7151 (tt) REVERT: A 985 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: A 1026 MET cc_start: 0.7529 (tpp) cc_final: 0.7115 (ttp) REVERT: B 242 HIS cc_start: 0.7512 (t70) cc_final: 0.7135 (t70) REVERT: B 453 PHE cc_start: 0.8516 (m-80) cc_final: 0.8075 (m-80) REVERT: B 461 PHE cc_start: 0.9067 (m-80) cc_final: 0.8419 (m-10) REVERT: B 1086 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6800 (m-10) REVERT: C 462 GLU cc_start: 0.8935 (tp30) cc_final: 0.8130 (tm-30) outliers start: 20 outliers final: 13 residues processed: 123 average time/residue: 0.3322 time to fit residues: 70.0631 Evaluate side-chains 115 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 1094 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 77 optimal weight: 0.0470 chunk 280 optimal weight: 0.9980 chunk 302 optimal weight: 0.8980 chunk 249 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25749 Z= 0.209 Angle : 0.556 11.972 35035 Z= 0.281 Chirality : 0.044 0.339 4199 Planarity : 0.003 0.043 4424 Dihedral : 6.834 56.666 4887 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.25 % Favored : 93.59 % Rotamer: Outliers : 1.18 % Allowed : 9.54 % Favored : 89.28 % 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: -0.59 (0.15), residues: 3040 helix: 1.48 (0.21), residues: 685 sheet: 0.03 (0.19), residues: 709 loop : -1.45 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 PHE 0.025 0.001 PHE A 389 TYR 0.013 0.001 TYR B1064 ARG 0.005 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0086 (pmm) cc_final: -0.0342 (pmm) REVERT: A 335 PHE cc_start: 0.7837 (m-80) cc_final: 0.7504 (m-80) REVERT: A 985 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: A 1026 MET cc_start: 0.7411 (tpp) cc_final: 0.6979 (ttp) REVERT: B 449 LEU cc_start: 0.9011 (pt) cc_final: 0.8462 (tt) REVERT: B 453 PHE cc_start: 0.8523 (m-80) cc_final: 0.8183 (m-80) REVERT: B 461 PHE cc_start: 0.9058 (m-80) cc_final: 0.8459 (m-10) REVERT: C 462 GLU cc_start: 0.8936 (tp30) cc_final: 0.8090 (tm-30) REVERT: C 875 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7947 (tp) outliers start: 32 outliers final: 19 residues processed: 136 average time/residue: 0.3278 time to fit residues: 77.3826 Evaluate side-chains 119 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 1094 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25749 Z= 0.225 Angle : 0.556 10.296 35035 Z= 0.280 Chirality : 0.044 0.329 4199 Planarity : 0.003 0.042 4424 Dihedral : 6.439 56.889 4887 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.45 % Favored : 93.45 % Rotamer: Outliers : 1.77 % Allowed : 11.02 % Favored : 87.21 % 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: -0.58 (0.15), residues: 3040 helix: 1.53 (0.21), residues: 677 sheet: 0.03 (0.19), residues: 708 loop : -1.44 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 PHE 0.024 0.001 PHE A1118 TYR 0.013 0.001 TYR B 91 ARG 0.003 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 109 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0160 (pmm) cc_final: -0.0211 (mpp) REVERT: A 694 MET cc_start: 0.7745 (mtp) cc_final: 0.7480 (mpp) REVERT: A 875 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7312 (tt) REVERT: A 985 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: A 1026 MET cc_start: 0.7485 (tpp) cc_final: 0.6963 (ttp) REVERT: B 449 LEU cc_start: 0.9046 (pt) cc_final: 0.8516 (tt) REVERT: B 453 PHE cc_start: 0.8506 (m-80) cc_final: 0.8198 (m-80) REVERT: B 461 PHE cc_start: 0.9046 (m-80) cc_final: 0.8460 (m-10) REVERT: B 739 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8545 (mp) REVERT: B 1086 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6717 (m-80) REVERT: C 449 LEU cc_start: 0.9381 (tp) cc_final: 0.9171 (tp) REVERT: C 462 GLU cc_start: 0.8879 (tp30) cc_final: 0.8110 (tm-30) REVERT: C 903 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6522 (m-10) REVERT: C 931 ILE cc_start: 0.8643 (mm) cc_final: 0.8426 (mm) outliers start: 48 outliers final: 26 residues processed: 150 average time/residue: 0.3050 time to fit residues: 80.0926 Evaluate side-chains 132 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1094 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 205 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 267 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 25749 Z= 0.441 Angle : 0.688 10.102 35035 Z= 0.352 Chirality : 0.048 0.318 4199 Planarity : 0.004 0.045 4424 Dihedral : 6.739 57.756 4887 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.70 % Favored : 92.14 % Rotamer: Outliers : 2.44 % Allowed : 12.98 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.98 (0.15), residues: 3040 helix: 1.10 (0.20), residues: 676 sheet: -0.14 (0.19), residues: 709 loop : -1.70 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 64 HIS 0.008 0.002 HIS A1085 PHE 0.042 0.002 PHE A1118 TYR 0.028 0.002 TYR B 91 ARG 0.005 0.000 ARG B 902 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 108 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0109 (pmm) cc_final: -0.0461 (mpp) REVERT: A 560 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6974 (mt0) REVERT: A 875 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6685 (tt) REVERT: A 993 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8317 (mt) REVERT: B 318 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7483 (mm-40) REVERT: B 449 LEU cc_start: 0.9066 (pt) cc_final: 0.8524 (tt) REVERT: B 453 PHE cc_start: 0.8545 (m-80) cc_final: 0.8233 (m-80) REVERT: B 461 PHE cc_start: 0.9021 (m-80) cc_final: 0.8413 (m-10) REVERT: B 983 LYS cc_start: 0.8483 (tppt) cc_final: 0.8165 (tppt) REVERT: B 1086 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6692 (m-10) REVERT: B 1129 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7383 (tp) REVERT: C 462 GLU cc_start: 0.8876 (tp30) cc_final: 0.8092 (tm-30) REVERT: C 999 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8241 (tp-100) outliers start: 66 outliers final: 44 residues processed: 163 average time/residue: 0.2938 time to fit residues: 85.5665 Evaluate side-chains 147 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 98 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 174 optimal weight: 0.0070 chunk 73 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 HIS ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25749 Z= 0.157 Angle : 0.557 9.551 35035 Z= 0.277 Chirality : 0.044 0.313 4199 Planarity : 0.003 0.044 4424 Dihedral : 6.246 57.927 4887 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.56 % Favored : 94.24 % Rotamer: Outliers : 1.89 % Allowed : 14.01 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3040 helix: 1.61 (0.21), residues: 667 sheet: -0.00 (0.20), residues: 685 loop : -1.49 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.011 0.001 HIS B 242 PHE 0.024 0.001 PHE A 389 TYR 0.013 0.001 TYR C 91 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 102 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0203 (pmm) cc_final: -0.0115 (mpp) REVERT: A 875 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7185 (tt) REVERT: A 1026 MET cc_start: 0.7446 (tpp) cc_final: 0.6941 (ttp) REVERT: B 318 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7463 (mm-40) REVERT: B 449 LEU cc_start: 0.9055 (pt) cc_final: 0.8534 (tt) REVERT: B 453 PHE cc_start: 0.8539 (m-80) cc_final: 0.8113 (m-80) REVERT: B 461 PHE cc_start: 0.9026 (m-80) cc_final: 0.8427 (m-10) REVERT: B 983 LYS cc_start: 0.8559 (tppt) cc_final: 0.8234 (tppt) REVERT: B 1026 MET cc_start: 0.8719 (tpp) cc_final: 0.8405 (tpt) REVERT: B 1129 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7382 (tp) REVERT: C 462 GLU cc_start: 0.8849 (tp30) cc_final: 0.8056 (tm-30) REVERT: C 999 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8154 (tp-100) outliers start: 51 outliers final: 36 residues processed: 142 average time/residue: 0.3189 time to fit residues: 79.9638 Evaluate side-chains 137 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 99 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 25749 Z= 0.286 Angle : 0.591 9.469 35035 Z= 0.296 Chirality : 0.045 0.306 4199 Planarity : 0.003 0.045 4424 Dihedral : 6.249 57.333 4887 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.71 % Favored : 93.12 % Rotamer: Outliers : 2.33 % Allowed : 14.12 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3040 helix: 1.52 (0.21), residues: 668 sheet: -0.03 (0.20), residues: 686 loop : -1.54 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.005 0.001 HIS A1085 PHE 0.030 0.001 PHE A1118 TYR 0.017 0.001 TYR B 91 ARG 0.003 0.000 ARG B 902 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 105 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0025 (pmm) cc_final: -0.0297 (mpp) REVERT: A 875 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7126 (tt) REVERT: A 1026 MET cc_start: 0.7551 (tpp) cc_final: 0.6963 (ttp) REVERT: B 318 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7496 (mm-40) REVERT: B 449 LEU cc_start: 0.9068 (pt) cc_final: 0.8552 (tt) REVERT: B 453 PHE cc_start: 0.8572 (m-80) cc_final: 0.8146 (m-80) REVERT: B 461 PHE cc_start: 0.8986 (m-80) cc_final: 0.8393 (m-10) REVERT: B 1086 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: B 1129 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7362 (tp) REVERT: C 462 GLU cc_start: 0.8892 (tp30) cc_final: 0.8093 (tm-30) REVERT: C 931 ILE cc_start: 0.8659 (mm) cc_final: 0.8392 (mm) REVERT: C 999 GLN cc_start: 0.8470 (tp-100) cc_final: 0.8208 (tp-100) outliers start: 63 outliers final: 49 residues processed: 157 average time/residue: 0.3042 time to fit residues: 84.9125 Evaluate side-chains 151 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 99 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 146 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 25749 Z= 0.195 Angle : 0.559 9.500 35035 Z= 0.278 Chirality : 0.044 0.302 4199 Planarity : 0.003 0.045 4424 Dihedral : 6.069 57.105 4887 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 2.40 % Allowed : 14.01 % Favored : 83.59 % 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: -0.61 (0.15), residues: 3040 helix: 1.65 (0.21), residues: 666 sheet: -0.01 (0.20), residues: 681 loop : -1.48 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.005 0.001 HIS B1085 PHE 0.027 0.001 PHE A 389 TYR 0.013 0.001 TYR A1064 ARG 0.002 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 102 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7263 (t0) cc_final: 0.7056 (t0) REVERT: A 153 MET cc_start: 0.0073 (pmm) cc_final: -0.0227 (mpp) REVERT: A 875 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7169 (tt) REVERT: A 998 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8377 (mm) REVERT: A 1026 MET cc_start: 0.7493 (tpp) cc_final: 0.6933 (ttp) REVERT: B 318 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7476 (mm-40) REVERT: B 449 LEU cc_start: 0.9065 (pt) cc_final: 0.8554 (tt) REVERT: B 453 PHE cc_start: 0.8580 (m-80) cc_final: 0.8165 (m-80) REVERT: B 461 PHE cc_start: 0.8979 (m-80) cc_final: 0.8397 (m-10) REVERT: B 983 LYS cc_start: 0.8390 (tppt) cc_final: 0.8100 (tppt) REVERT: B 1129 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7473 (tp) REVERT: C 29 THR cc_start: 0.6936 (OUTLIER) cc_final: 0.6599 (p) REVERT: C 462 GLU cc_start: 0.8871 (tp30) cc_final: 0.8062 (tm-30) REVERT: C 931 ILE cc_start: 0.8643 (mm) cc_final: 0.8430 (mm) REVERT: C 999 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8242 (tp-100) outliers start: 65 outliers final: 52 residues processed: 156 average time/residue: 0.3051 time to fit residues: 85.3854 Evaluate side-chains 156 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 100 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.9980 chunk 284 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 276 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 84 optimal weight: 0.2980 chunk 249 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 275 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25749 Z= 0.165 Angle : 0.544 9.519 35035 Z= 0.269 Chirality : 0.044 0.300 4199 Planarity : 0.003 0.046 4424 Dihedral : 5.872 57.033 4887 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.02 % Favored : 93.82 % Rotamer: Outliers : 2.33 % Allowed : 14.27 % Favored : 83.40 % 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: -0.48 (0.15), residues: 3040 helix: 1.73 (0.21), residues: 669 sheet: 0.07 (0.20), residues: 682 loop : -1.40 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 PHE 0.025 0.001 PHE A 389 TYR 0.013 0.001 TYR A1064 ARG 0.002 0.000 ARG C 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 103 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0109 (pmm) cc_final: -0.0181 (mpp) REVERT: A 875 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7393 (tt) REVERT: A 998 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8374 (mm) REVERT: A 1026 MET cc_start: 0.7539 (tpp) cc_final: 0.6982 (ttp) REVERT: B 318 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7450 (mm-40) REVERT: B 449 LEU cc_start: 0.8939 (pt) cc_final: 0.8407 (tt) REVERT: B 453 PHE cc_start: 0.8584 (m-80) cc_final: 0.8171 (m-80) REVERT: B 461 PHE cc_start: 0.8993 (m-80) cc_final: 0.8439 (m-10) REVERT: B 983 LYS cc_start: 0.8437 (tppt) cc_final: 0.8155 (tppt) REVERT: B 1129 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7640 (tp) REVERT: C 29 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6482 (p) REVERT: C 453 PHE cc_start: 0.8718 (m-10) cc_final: 0.8457 (m-10) REVERT: C 462 GLU cc_start: 0.8870 (tp30) cc_final: 0.8043 (tm-30) REVERT: C 931 ILE cc_start: 0.8639 (mm) cc_final: 0.8418 (mm) REVERT: C 999 GLN cc_start: 0.8434 (tp-100) cc_final: 0.8220 (tp-100) outliers start: 63 outliers final: 52 residues processed: 156 average time/residue: 0.3001 time to fit residues: 83.5216 Evaluate side-chains 155 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 99 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.7980 chunk 292 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 282 optimal weight: 0.0970 chunk 244 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25749 Z= 0.178 Angle : 0.545 9.508 35035 Z= 0.270 Chirality : 0.043 0.302 4199 Planarity : 0.003 0.045 4424 Dihedral : 5.792 57.059 4887 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.02 % Favored : 93.82 % Rotamer: Outliers : 2.11 % Allowed : 14.64 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3040 helix: 1.76 (0.21), residues: 668 sheet: 0.10 (0.20), residues: 672 loop : -1.36 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 PHE 0.026 0.001 PHE A 389 TYR 0.013 0.001 TYR A1064 ARG 0.002 0.000 ARG C 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 106 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0166 (pmm) cc_final: -0.0114 (mpp) REVERT: A 875 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7418 (tt) REVERT: A 998 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8336 (mm) REVERT: A 1026 MET cc_start: 0.7551 (tpp) cc_final: 0.6970 (ttp) REVERT: B 318 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7448 (mm-40) REVERT: B 449 LEU cc_start: 0.8864 (pt) cc_final: 0.8319 (tt) REVERT: B 453 PHE cc_start: 0.8593 (m-80) cc_final: 0.8179 (m-80) REVERT: B 461 PHE cc_start: 0.8977 (m-80) cc_final: 0.8420 (m-10) REVERT: B 983 LYS cc_start: 0.8438 (tppt) cc_final: 0.8150 (tppt) REVERT: B 1086 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6305 (m-80) REVERT: B 1129 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7650 (tp) REVERT: C 29 THR cc_start: 0.6826 (OUTLIER) cc_final: 0.6472 (p) REVERT: C 453 PHE cc_start: 0.8769 (m-10) cc_final: 0.8524 (m-10) REVERT: C 462 GLU cc_start: 0.8854 (tp30) cc_final: 0.7997 (tm-30) REVERT: C 931 ILE cc_start: 0.8637 (mm) cc_final: 0.8418 (mm) outliers start: 57 outliers final: 51 residues processed: 155 average time/residue: 0.2981 time to fit residues: 81.8499 Evaluate side-chains 155 residues out of total 2705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 99 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 244 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.115881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.072575 restraints weight = 60868.259| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.74 r_work: 0.3150 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 25749 Z= 0.361 Angle : 0.627 9.427 35035 Z= 0.317 Chirality : 0.046 0.298 4199 Planarity : 0.004 0.044 4424 Dihedral : 6.078 57.632 4887 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.11 % Favored : 92.73 % Rotamer: Outliers : 2.33 % Allowed : 14.49 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3040 helix: 1.49 (0.21), residues: 667 sheet: -0.04 (0.20), residues: 681 loop : -1.51 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 64 HIS 0.008 0.001 HIS C1085 PHE 0.037 0.002 PHE A1118 TYR 0.023 0.002 TYR B 91 ARG 0.003 0.000 ARG B 902 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4780.04 seconds wall clock time: 88 minutes 16.69 seconds (5296.69 seconds total)