Starting phenix.real_space_refine on Mon Feb 19 16:49:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v77_31761/02_2024/7v77_31761.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v77_31761/02_2024/7v77_31761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v77_31761/02_2024/7v77_31761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v77_31761/02_2024/7v77_31761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v77_31761/02_2024/7v77_31761.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v77_31761/02_2024/7v77_31761.pdb" } resolution = 3.3 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= 0.052 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 16089 2.51 5 N 4099 2.21 5 O 4994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25293 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} 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: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.05, per 1000 atoms: 0.52 Number of scatterers: 25293 At special positions: 0 Unit cell: (141.9, 150.7, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4994 8.00 N 4099 7.00 C 16089 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=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.02 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.02 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 234 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " 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 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 234 " " NAG C2005 " - " ASN C 340 " " NAG C2006 " - " ASN C 600 " " NAG C2007 " - " 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 O 1 " - " ASN B 165 " " 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 328 " " NAG a 1 " - " ASN C 613 " " NAG b 1 " - " ASN C 706 " " NAG c 1 " - " ASN C 714 " " NAG d 1 " - " ASN C 798 " " NAG e 1 " - " ASN C1071 " " NAG f 1 " - " ASN C1095 " " NAG g 1 " - " ASN C1131 " Time building additional restraints: 10.60 Conformation dependent library (CDL) restraints added in 4.5 seconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5796 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 46 sheets defined 24.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 removed outlier: 3.589A pdb=" N THR A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.564A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 340' Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.329A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.226A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.510A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.502A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.947A 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 removed outlier: 3.544A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.645A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 906 removed outlier: 4.137A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.526A 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: 3.551A 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: 3.578A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.400A pdb=" N VAL A 988 " --> pdb=" O PRO 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 335 through 340 Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.575A pdb=" N SER B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.588A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 removed outlier: 3.670A pdb=" N GLU B 403 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.547A 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 743 through 752 removed outlier: 3.840A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.644A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.704A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 895 through 905 removed outlier: 4.033A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.816A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.872A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.484A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.980A 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: 3.865A 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 361 through 368 removed outlier: 4.074A pdb=" N LEU C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.595A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 4.254A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 764 " --> pdb=" O LEU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.589A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 895 through 906 removed outlier: 4.145A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.838A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.950A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 removed outlier: 3.790A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.186A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.363A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.692A 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: 7.124A 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: 4.031A 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: 4.386A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.230A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.751A 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 removed outlier: 3.620A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.603A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) 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: 4.089A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 43 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.889A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 725 removed outlier: 3.561A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.512A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 786 removed outlier: 5.699A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.835A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.705A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.060A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.834A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.623A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.817A 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: 4.225A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 325 removed outlier: 5.450A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.434A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC8, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC9, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.060A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AD2, first strand: chain 'B' and resid 714 through 725 removed outlier: 6.079A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.481A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 3.514A pdb=" N SER B1120 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1091 through 1094 removed outlier: 4.763A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.827A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.951A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.319A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.920A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 307 through 316 removed outlier: 3.536A pdb=" N THR C 312 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 322 through 323 Processing sheet with id=AE2, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE3, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE4, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE5, first strand: chain 'C' and resid 562 through 564 removed outlier: 4.051A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.308A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.723A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.402A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.113A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1091 through 1094 964 hydrogen bonds defined for protein. 2640 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: 10.41 Time building geometry restraints manager: 11.34 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: 7962 1.34 - 1.46: 6376 1.46 - 1.58: 11378 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25854 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" C PRO A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 1.372 -0.039 2.34e-02 1.83e+03 2.72e+00 bond pdb=" C1 NAG e 1 " pdb=" O5 NAG e 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 25849 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.63: 517 105.63 - 112.73: 14111 112.73 - 119.82: 7910 119.82 - 126.92: 12423 126.92 - 134.02: 230 Bond angle restraints: 35191 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.65e+00 angle pdb=" CA CYS B 522 " pdb=" CB CYS B 522 " pdb=" SG CYS B 522 " ideal model delta sigma weight residual 114.40 120.69 -6.29 2.30e+00 1.89e-01 7.48e+00 angle pdb=" N PRO A 983 " pdb=" CA PRO A 983 " pdb=" C PRO A 983 " ideal model delta sigma weight residual 110.70 113.88 -3.18 1.22e+00 6.72e-01 6.81e+00 angle pdb=" CA CYS B 388 " pdb=" CB CYS B 388 " pdb=" SG CYS B 388 " ideal model delta sigma weight residual 114.40 120.09 -5.69 2.30e+00 1.89e-01 6.11e+00 angle pdb=" CA CYS C 131 " pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " ideal model delta sigma weight residual 114.40 119.98 -5.58 2.30e+00 1.89e-01 5.89e+00 ... (remaining 35186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 15285 22.70 - 45.41: 907 45.41 - 68.11: 122 68.11 - 90.81: 27 90.81 - 113.52: 17 Dihedral angle restraints: 16358 sinusoidal: 7340 harmonic: 9018 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -174.96 88.96 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 1.96 -87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS C 388 " pdb=" SG CYS C 388 " pdb=" SG CYS C 522 " pdb=" CB CYS C 522 " ideal model delta sinusoidal sigma weight residual -86.00 0.63 -86.63 1 1.00e+01 1.00e-02 9.04e+01 ... (remaining 16355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 4185 0.131 - 0.263: 32 0.263 - 0.394: 0 0.394 - 0.526: 0 0.526 - 0.657: 1 Chirality restraints: 4218 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 -1.74 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG C2002 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C2002 " pdb=" O5 NAG C2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4215 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 138 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO C 139 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 216 " -0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO A 217 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1071 " -0.021 2.00e-02 2.50e+03 1.95e-02 4.74e+00 pdb=" CG ASN B1071 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B1071 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B1071 " 0.022 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.021 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 376 2.64 - 3.21: 23168 3.21 - 3.77: 36542 3.77 - 4.34: 49482 4.34 - 4.90: 82466 Nonbonded interactions: 192034 Sorted by model distance: nonbonded pdb=" OD2 ASP A 575 " pdb=" OG1 THR A 578 " model vdw 2.077 2.440 nonbonded pdb=" OD2 ASP C 575 " pdb=" OG1 THR C 578 " model vdw 2.119 2.440 nonbonded pdb=" OD1 ASP B 53 " pdb=" N LEU B 54 " model vdw 2.137 2.520 nonbonded pdb=" NH1 ARG A 902 " pdb=" O LEU A1046 " model vdw 2.181 2.520 nonbonded pdb=" O GLU C 658 " pdb=" OH TYR C 692 " model vdw 2.181 2.440 ... (remaining 192029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 618 or resid 632 through 824 or resid 852 throu \ gh 1143 or resid 2001 through 2004)) selection = (chain 'C' and (resid 14 through 1143 or resid 2001 through 2004)) } 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' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.150 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 66.610 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.410 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 0.054 25854 Z= 0.336 Angle : 0.648 7.807 35191 Z= 0.326 Chirality : 0.048 0.657 4218 Planarity : 0.004 0.075 4447 Dihedral : 13.975 113.515 10442 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.22 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.49 (0.15), residues: 3054 helix: 1.47 (0.21), residues: 669 sheet: 0.34 (0.20), residues: 694 loop : -1.43 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 883 HIS 0.003 0.001 HIS A1061 PHE 0.029 0.001 PHE C 903 TYR 0.017 0.001 TYR C 870 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8287 (m-80) cc_final: 0.8016 (m-80) REVERT: A 106 PHE cc_start: 0.5534 (m-80) cc_final: 0.5332 (m-80) REVERT: A 237 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7641 (ptp-170) REVERT: B 52 GLN cc_start: 0.8665 (pp30) cc_final: 0.8165 (pp30) REVERT: B 153 MET cc_start: 0.4158 (pmm) cc_final: 0.3494 (pmm) REVERT: B 433 TRP cc_start: 0.7500 (p90) cc_final: 0.7125 (p90) REVERT: B 630 TRP cc_start: 0.6770 (m-10) cc_final: 0.6194 (m100) REVERT: B 773 LYS cc_start: 0.8792 (tmmt) cc_final: 0.8544 (tmmt) REVERT: B 866 MET cc_start: 0.8560 (mtm) cc_final: 0.8347 (mtt) REVERT: B 883 TRP cc_start: 0.7689 (p90) cc_final: 0.7221 (p90) REVERT: C 140 PHE cc_start: 0.7878 (p90) cc_final: 0.7624 (p90) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3344 time to fit residues: 93.0381 Evaluate side-chains 123 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.0980 chunk 234 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 242 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 147 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25854 Z= 0.185 Angle : 0.556 9.112 35191 Z= 0.276 Chirality : 0.045 0.473 4218 Planarity : 0.004 0.051 4447 Dihedral : 8.964 102.908 4942 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.28 % Rotamer: Outliers : 0.26 % Allowed : 6.36 % Favored : 93.39 % 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: -0.41 (0.15), residues: 3054 helix: 1.64 (0.21), residues: 670 sheet: 0.30 (0.19), residues: 717 loop : -1.40 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 883 HIS 0.004 0.001 HIS B 66 PHE 0.024 0.001 PHE A 55 TYR 0.020 0.001 TYR C1064 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8263 (m-80) cc_final: 0.8004 (m-80) REVERT: A 200 TYR cc_start: 0.7258 (m-80) cc_final: 0.7052 (t80) REVERT: A 237 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7868 (ptp-170) REVERT: A 899 MET cc_start: 0.7989 (mmt) cc_final: 0.7698 (mmt) REVERT: B 52 GLN cc_start: 0.8643 (pp30) cc_final: 0.8148 (pp30) REVERT: B 153 MET cc_start: 0.4195 (pmm) cc_final: 0.3763 (pmm) REVERT: B 379 VAL cc_start: 0.8671 (m) cc_final: 0.8401 (m) REVERT: B 433 TRP cc_start: 0.7448 (p90) cc_final: 0.7122 (p90) REVERT: B 630 TRP cc_start: 0.6986 (m-10) cc_final: 0.6457 (m100) REVERT: B 866 MET cc_start: 0.8394 (mtm) cc_final: 0.8126 (mtt) REVERT: B 883 TRP cc_start: 0.7684 (p90) cc_final: 0.7242 (p90) REVERT: C 980 ARG cc_start: 0.8096 (ttt-90) cc_final: 0.7513 (ttp-170) outliers start: 7 outliers final: 3 residues processed: 146 average time/residue: 0.3412 time to fit residues: 83.6143 Evaluate side-chains 125 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain B residue 299 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.0070 chunk 87 optimal weight: 0.0170 chunk 233 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 281 optimal weight: 0.0770 chunk 303 optimal weight: 0.6980 chunk 250 optimal weight: 40.0000 chunk 278 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 GLN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25854 Z= 0.131 Angle : 0.513 10.525 35191 Z= 0.251 Chirality : 0.044 0.451 4218 Planarity : 0.003 0.045 4447 Dihedral : 8.093 100.729 4942 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 0.74 % Allowed : 8.50 % Favored : 90.76 % 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: -0.24 (0.15), residues: 3054 helix: 1.89 (0.21), residues: 670 sheet: 0.37 (0.19), residues: 713 loop : -1.33 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 883 HIS 0.002 0.000 HIS B 66 PHE 0.029 0.001 PHE C 238 TYR 0.016 0.001 TYR C1064 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8180 (m-80) cc_final: 0.7889 (m-80) REVERT: A 189 LEU cc_start: 0.7847 (tt) cc_final: 0.7504 (tp) REVERT: A 200 TYR cc_start: 0.7271 (m-80) cc_final: 0.6949 (t80) REVERT: A 237 ARG cc_start: 0.8263 (mtp180) cc_final: 0.7896 (ptp-170) REVERT: B 52 GLN cc_start: 0.8561 (pp30) cc_final: 0.8240 (pp30) REVERT: B 239 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.6241 (mm110) REVERT: B 379 VAL cc_start: 0.8715 (m) cc_final: 0.8431 (m) REVERT: B 389 PHE cc_start: 0.5695 (m-80) cc_final: 0.5459 (m-80) REVERT: B 433 TRP cc_start: 0.7513 (p90) cc_final: 0.7167 (p90) REVERT: B 630 TRP cc_start: 0.6947 (m-10) cc_final: 0.6443 (m100) REVERT: B 883 TRP cc_start: 0.7616 (p90) cc_final: 0.7151 (p90) REVERT: B 985 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7521 (mp0) REVERT: C 883 TRP cc_start: 0.7915 (p90) cc_final: 0.7712 (p90) REVERT: C 980 ARG cc_start: 0.8080 (ttt-90) cc_final: 0.7546 (ttp-170) REVERT: C 1026 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7799 (ttp) outliers start: 20 outliers final: 8 residues processed: 164 average time/residue: 0.3463 time to fit residues: 94.7941 Evaluate side-chains 134 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 1.9990 chunk 211 optimal weight: 0.0000 chunk 145 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 282 optimal weight: 0.5980 chunk 298 optimal weight: 0.0570 chunk 147 optimal weight: 10.0000 chunk 267 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.7306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25854 Z= 0.171 Angle : 0.528 11.339 35191 Z= 0.259 Chirality : 0.044 0.443 4218 Planarity : 0.003 0.047 4447 Dihedral : 7.522 95.621 4942 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 1.07 % Allowed : 10.24 % Favored : 88.69 % 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: -0.24 (0.15), residues: 3054 helix: 1.85 (0.21), residues: 672 sheet: 0.37 (0.19), residues: 722 loop : -1.32 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 883 HIS 0.003 0.001 HIS B1085 PHE 0.018 0.001 PHE A 55 TYR 0.026 0.001 TYR B 450 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8260 (m-80) cc_final: 0.7963 (m-80) REVERT: A 189 LEU cc_start: 0.7890 (tt) cc_final: 0.7553 (tp) REVERT: A 200 TYR cc_start: 0.7240 (m-80) cc_final: 0.6942 (t80) REVERT: A 237 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7832 (ptp-170) REVERT: A 875 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7506 (tt) REVERT: A 897 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7245 (ptp) REVERT: B 52 GLN cc_start: 0.8623 (pp30) cc_final: 0.8059 (pp30) REVERT: B 379 VAL cc_start: 0.8718 (m) cc_final: 0.8432 (m) REVERT: B 389 PHE cc_start: 0.5562 (m-80) cc_final: 0.5317 (m-80) REVERT: B 433 TRP cc_start: 0.7521 (p90) cc_final: 0.7164 (p90) REVERT: B 630 TRP cc_start: 0.6982 (m-10) cc_final: 0.6526 (m100) REVERT: B 883 TRP cc_start: 0.7829 (p90) cc_final: 0.7370 (p90) REVERT: B 985 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7568 (mp0) REVERT: C 53 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6622 (m-30) REVERT: C 883 TRP cc_start: 0.7947 (p90) cc_final: 0.7726 (p90) REVERT: C 980 ARG cc_start: 0.8093 (ttt-90) cc_final: 0.7546 (ttp-170) REVERT: C 1026 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7818 (ttp) outliers start: 29 outliers final: 12 residues processed: 156 average time/residue: 0.3122 time to fit residues: 83.4809 Evaluate side-chains 135 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 30.0000 chunk 169 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 152 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 ASN A 911 ASN A1045 HIS ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN B 898 GLN B 999 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 25854 Z= 0.592 Angle : 0.755 12.439 35191 Z= 0.381 Chirality : 0.052 0.437 4218 Planarity : 0.005 0.049 4447 Dihedral : 7.740 99.135 4942 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.27 % Favored : 92.63 % Rotamer: Outliers : 2.00 % Allowed : 12.23 % Favored : 85.77 % 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: -0.90 (0.15), residues: 3054 helix: 1.07 (0.21), residues: 659 sheet: -0.06 (0.19), residues: 699 loop : -1.57 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 883 HIS 0.007 0.002 HIS B1045 PHE 0.045 0.003 PHE C1086 TYR 0.031 0.002 TYR C1064 ARG 0.015 0.001 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 121 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7914 (tt) cc_final: 0.7586 (tp) REVERT: A 270 ARG cc_start: 0.6667 (ptm160) cc_final: 0.6225 (ptm160) REVERT: A 875 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7646 (tt) REVERT: B 52 GLN cc_start: 0.8706 (pp30) cc_final: 0.8155 (pp30) REVERT: B 393 TYR cc_start: 0.7914 (m-10) cc_final: 0.7354 (m-10) REVERT: B 433 TRP cc_start: 0.7549 (p90) cc_final: 0.7136 (p90) REVERT: B 630 TRP cc_start: 0.6797 (m-10) cc_final: 0.6123 (m100) REVERT: C 561 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7163 (mt0) REVERT: C 875 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7717 (tt) outliers start: 54 outliers final: 35 residues processed: 169 average time/residue: 0.3154 time to fit residues: 92.7494 Evaluate side-chains 152 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1086 PHE Chi-restraints excluded: chain C residue 1111 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 298 optimal weight: 0.6980 chunk 248 optimal weight: 20.0000 chunk 138 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 ASN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25854 Z= 0.157 Angle : 0.549 9.074 35191 Z= 0.272 Chirality : 0.044 0.433 4218 Planarity : 0.003 0.043 4447 Dihedral : 7.065 94.180 4942 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 1.55 % Allowed : 13.41 % Favored : 85.03 % 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: -0.52 (0.15), residues: 3054 helix: 1.69 (0.21), residues: 661 sheet: 0.10 (0.19), residues: 707 loop : -1.44 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 883 HIS 0.003 0.001 HIS B1085 PHE 0.017 0.001 PHE A 55 TYR 0.018 0.001 TYR C1064 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7911 (tt) cc_final: 0.7564 (tp) REVERT: A 237 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7837 (ptp-170) REVERT: A 875 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7622 (tt) REVERT: A 899 MET cc_start: 0.8016 (mmt) cc_final: 0.7570 (mmt) REVERT: B 52 GLN cc_start: 0.8639 (pp30) cc_final: 0.8082 (pp30) REVERT: B 393 TYR cc_start: 0.7869 (m-10) cc_final: 0.7407 (m-10) REVERT: B 433 TRP cc_start: 0.7582 (p90) cc_final: 0.7202 (p90) REVERT: B 630 TRP cc_start: 0.7008 (m-10) cc_final: 0.6447 (m100) REVERT: B 875 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8078 (tt) REVERT: C 53 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: C 561 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7085 (mt0) outliers start: 42 outliers final: 27 residues processed: 163 average time/residue: 0.3105 time to fit residues: 88.3173 Evaluate side-chains 144 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 2.9990 chunk 33 optimal weight: 30.0000 chunk 170 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 251 optimal weight: 40.0000 chunk 166 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN B 239 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 25854 Z= 0.471 Angle : 0.675 10.795 35191 Z= 0.339 Chirality : 0.049 0.426 4218 Planarity : 0.004 0.044 4447 Dihedral : 7.338 92.237 4942 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.17 % Favored : 92.73 % Rotamer: Outliers : 2.22 % Allowed : 13.75 % Favored : 84.04 % 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: -0.81 (0.15), residues: 3054 helix: 1.31 (0.21), residues: 661 sheet: -0.01 (0.20), residues: 682 loop : -1.57 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 883 HIS 0.005 0.001 HIS B1045 PHE 0.043 0.002 PHE C1086 TYR 0.027 0.002 TYR C1064 ARG 0.010 0.001 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 122 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7914 (tt) cc_final: 0.7589 (tp) REVERT: A 875 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7664 (tt) REVERT: A 1129 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8072 (pt) REVERT: B 52 GLN cc_start: 0.8658 (pp30) cc_final: 0.8109 (pp30) REVERT: B 393 TYR cc_start: 0.7874 (m-10) cc_final: 0.7312 (m-10) REVERT: B 433 TRP cc_start: 0.7587 (p90) cc_final: 0.7156 (p90) REVERT: B 630 TRP cc_start: 0.7066 (m-10) cc_final: 0.6419 (m100) outliers start: 60 outliers final: 45 residues processed: 174 average time/residue: 0.3005 time to fit residues: 91.4059 Evaluate side-chains 164 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 117 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1086 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 189 optimal weight: 0.0770 chunk 202 optimal weight: 0.5980 chunk 147 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25854 Z= 0.157 Angle : 0.545 9.018 35191 Z= 0.270 Chirality : 0.044 0.427 4218 Planarity : 0.003 0.043 4447 Dihedral : 6.773 85.426 4942 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 1.44 % Allowed : 14.56 % Favored : 84.00 % 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: -0.51 (0.15), residues: 3054 helix: 1.79 (0.21), residues: 655 sheet: 0.05 (0.19), residues: 711 loop : -1.44 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 883 HIS 0.004 0.001 HIS B1085 PHE 0.016 0.001 PHE C 201 TYR 0.018 0.001 TYR C1064 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7900 (tt) cc_final: 0.7553 (tp) REVERT: A 875 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7610 (tt) REVERT: A 899 MET cc_start: 0.8092 (mmt) cc_final: 0.7641 (mmt) REVERT: B 52 GLN cc_start: 0.8649 (pp30) cc_final: 0.8091 (pp30) REVERT: B 393 TYR cc_start: 0.7693 (m-10) cc_final: 0.7084 (m-10) REVERT: B 433 TRP cc_start: 0.7595 (p90) cc_final: 0.7191 (p90) REVERT: B 630 TRP cc_start: 0.7057 (m-10) cc_final: 0.6501 (m100) REVERT: B 875 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8153 (tt) REVERT: C 53 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6791 (m-30) REVERT: C 561 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7124 (mt0) outliers start: 39 outliers final: 26 residues processed: 161 average time/residue: 0.3161 time to fit residues: 88.8731 Evaluate side-chains 149 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.9990 chunk 285 optimal weight: 0.1980 chunk 260 optimal weight: 4.9990 chunk 277 optimal weight: 0.6980 chunk 167 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 85 optimal weight: 0.0050 chunk 250 optimal weight: 40.0000 chunk 262 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25854 Z= 0.145 Angle : 0.521 8.976 35191 Z= 0.257 Chirality : 0.043 0.426 4218 Planarity : 0.003 0.044 4447 Dihedral : 6.278 75.542 4942 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.17 % Favored : 94.73 % Rotamer: Outliers : 1.48 % Allowed : 14.75 % Favored : 83.78 % 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: -0.35 (0.15), residues: 3054 helix: 1.97 (0.21), residues: 654 sheet: 0.15 (0.19), residues: 714 loop : -1.36 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.002 0.000 HIS B1045 PHE 0.016 0.001 PHE C 201 TYR 0.027 0.001 TYR B 170 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7946 (tt) cc_final: 0.7607 (tp) REVERT: A 200 TYR cc_start: 0.7212 (m-80) cc_final: 0.6991 (t80) REVERT: A 875 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7651 (tt) REVERT: A 899 MET cc_start: 0.8177 (mmt) cc_final: 0.7958 (mmt) REVERT: B 52 GLN cc_start: 0.8679 (pp30) cc_final: 0.8195 (pp30) REVERT: B 433 TRP cc_start: 0.7534 (p90) cc_final: 0.7086 (p90) REVERT: B 630 TRP cc_start: 0.7130 (m-10) cc_final: 0.6597 (m100) REVERT: B 875 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8212 (tt) REVERT: C 53 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: C 118 LEU cc_start: 0.7157 (tt) cc_final: 0.6247 (mp) REVERT: C 561 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7069 (mt0) outliers start: 40 outliers final: 31 residues processed: 168 average time/residue: 0.3058 time to fit residues: 90.3446 Evaluate side-chains 154 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 245 optimal weight: 50.0000 chunk 25 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 HIS ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25854 Z= 0.321 Angle : 0.595 9.886 35191 Z= 0.296 Chirality : 0.046 0.419 4218 Planarity : 0.004 0.044 4447 Dihedral : 6.429 72.375 4942 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.86 % Favored : 94.04 % Rotamer: Outliers : 1.55 % Allowed : 15.04 % Favored : 83.41 % 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: -0.53 (0.15), residues: 3054 helix: 1.68 (0.21), residues: 649 sheet: 0.10 (0.19), residues: 705 loop : -1.42 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 883 HIS 0.005 0.001 HIS A1061 PHE 0.034 0.002 PHE C 192 TYR 0.033 0.001 TYR B 450 ARG 0.006 0.000 ARG C1036 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7849 (tt) cc_final: 0.7544 (tp) REVERT: A 875 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7621 (tt) REVERT: A 899 MET cc_start: 0.8086 (mmt) cc_final: 0.7648 (mmt) REVERT: B 52 GLN cc_start: 0.8671 (pp30) cc_final: 0.8116 (pp30) REVERT: B 393 TYR cc_start: 0.7637 (m-10) cc_final: 0.7148 (m-10) REVERT: B 433 TRP cc_start: 0.7535 (p90) cc_final: 0.7082 (p90) REVERT: B 875 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8224 (tt) REVERT: B 897 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7600 (ttm) REVERT: C 53 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6839 (m-30) REVERT: C 561 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7059 (mt0) outliers start: 42 outliers final: 35 residues processed: 162 average time/residue: 0.3012 time to fit residues: 86.2028 Evaluate side-chains 158 residues out of total 2706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 119 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 226 optimal weight: 5.9990 chunk 36 optimal weight: 50.0000 chunk 68 optimal weight: 1.9990 chunk 245 optimal weight: 50.0000 chunk 102 optimal weight: 3.9990 chunk 252 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.177925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.114732 restraints weight = 41102.380| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.52 r_work: 0.3469 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25854 Z= 0.320 Angle : 0.601 9.963 35191 Z= 0.299 Chirality : 0.046 0.413 4218 Planarity : 0.004 0.044 4447 Dihedral : 6.494 64.724 4942 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.12 % Favored : 93.78 % Rotamer: Outliers : 1.74 % Allowed : 15.00 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3054 helix: 1.55 (0.21), residues: 649 sheet: 0.00 (0.19), residues: 691 loop : -1.46 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 883 HIS 0.004 0.001 HIS A1085 PHE 0.030 0.002 PHE C 192 TYR 0.024 0.001 TYR B 450 ARG 0.007 0.000 ARG C1036 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4674.87 seconds wall clock time: 88 minutes 7.56 seconds (5287.56 seconds total)