Starting phenix.real_space_refine on Mon Feb 19 15:15:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edf_31069/02_2024/7edf_31069.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edf_31069/02_2024/7edf_31069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edf_31069/02_2024/7edf_31069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edf_31069/02_2024/7edf_31069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edf_31069/02_2024/7edf_31069.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edf_31069/02_2024/7edf_31069.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.057 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 109 5.16 5 C 15953 2.51 5 N 4057 2.21 5 O 4971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C GLU 513": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25090 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8077 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 51, 'TRANS': 983} Chain breaks: 6 Chain: "B" Number of atoms: 7986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7986 Classifications: {'peptide': 1022} Link IDs: {'PTRANS': 50, 'TRANS': 971} Chain breaks: 8 Chain: "C" Number of atoms: 7882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7882 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 50, 'TRANS': 957} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 12.81, per 1000 atoms: 0.51 Number of scatterers: 25090 At special positions: 0 Unit cell: (135.3, 137.5, 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 109 16.00 O 4971 8.00 N 4057 7.00 C 15953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 162 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 162 " " NAG B2003 " - " ASN B 231 " " NAG B2004 " - " ASN B 328 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 162 " " NAG C2003 " - " ASN C 328 " " NAG C2004 " - " ASN C 600 " " NAG C2005 " - " ASN C 654 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 231 " " NAG F 1 " - " ASN A 279 " " NAG G 1 " - " ASN A 328 " " NAG H 1 " - " ASN A 340 " " NAG I 1 " - " ASN A 613 " " NAG J 1 " - " ASN A 706 " " NAG K 1 " - " ASN A 714 " " NAG L 1 " - " ASN A 798 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN A1095 " " NAG O 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 120 " " NAG Q 1 " - " ASN B 279 " " NAG R 1 " - " ASN B 340 " " NAG S 1 " - " ASN B 613 " " NAG T 1 " - " ASN B 706 " " NAG U 1 " - " ASN B 714 " " NAG V 1 " - " ASN B 798 " " NAG W 1 " - " ASN B1071 " " NAG X 1 " - " ASN B1095 " " NAG Y 1 " - " ASN B1131 " " NAG Z 1 " - " ASN C 120 " " NAG a 1 " - " ASN C 231 " " NAG b 1 " - " ASN C 279 " " NAG c 1 " - " ASN C 340 " " NAG d 1 " - " ASN C 613 " " NAG e 1 " - " ASN C 706 " " NAG f 1 " - " ASN C 714 " " NAG g 1 " - " ASN C 798 " " NAG h 1 " - " ASN C1071 " " NAG i 1 " - " ASN C1095 " " NAG j 1 " - " ASN C1131 " Time building additional restraints: 11.05 Conformation dependent library (CDL) restraints added in 4.7 seconds 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5734 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 46 sheets defined 23.7% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.670A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 744 through 751 removed outlier: 3.517A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.877A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 822 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.853A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 943 through 961 removed outlier: 3.739A pdb=" N ASP A 947 " --> pdb=" O GLY A 943 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.680A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 removed outlier: 4.083A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1030 removed outlier: 3.839A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 removed outlier: 4.191A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.841A pdb=" N TRP B 350 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.527A pdb=" N ASN B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.586A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.753A pdb=" N VAL B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 757 through 780 Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.600A pdb=" N ILE B 847 " --> pdb=" O ARG B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 888 removed outlier: 4.270A pdb=" N GLY B 888 " --> pdb=" O PHE B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.509A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 907 No H-bonds generated for 'chain 'B' and resid 905 through 907' Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.767A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 936 Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.681A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 962 " --> pdb=" O THR B 958 " (cutoff:3.500A) 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 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.335A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.736A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 383 through 386 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.639A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.578A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.925A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 762 " --> pdb=" O THR C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 822 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.579A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.800A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.654A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.868A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 removed outlier: 3.591A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.613A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.908A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C1143 " --> pdb=" O GLN C1139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.151A pdb=" N PHE A 43 " --> pdb=" O ARG C 564 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP C 565 " --> pdb=" O THR C 570 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR C 570 " --> pdb=" O ASP C 565 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ASN C 537 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.552A pdb=" N VAL A 47 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.182A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 190 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 188 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 205 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 131 through 133 removed outlier: 6.110A pdb=" N GLN A 132 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.633A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.602A pdb=" N PHE A 538 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 545 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.025A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.079A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'A' and resid 562 through 563 removed outlier: 7.189A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.633A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 698 through 699 removed outlier: 7.007A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 709 through 712 Processing sheet with id=AB8, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.701A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AC1, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 5.073A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.195A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 264 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE B 65 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 200 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 224 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.814A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.706A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 645 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 320 through 325 removed outlier: 6.207A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN B 537 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.005A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.044A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 698 through 701 removed outlier: 6.845A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N LYS C 787 " --> pdb=" O ALA B 698 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN B 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 714 through 725 removed outlier: 3.504A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.681A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1073 through 1075 removed outlier: 3.873A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.990A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 224 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.944A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.010A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.764A pdb=" N SER C 159 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.685A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE5, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AE6, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.456A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.997A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.997A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.616A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.825A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) 865 hydrogen bonds defined for protein. 2349 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: 10.50 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7903 1.35 - 1.47: 6641 1.47 - 1.60: 10955 1.60 - 1.72: 0 1.72 - 1.84: 134 Bond restraints: 25633 Sorted by residual: bond pdb=" C PRO A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.332 1.365 -0.033 8.20e-03 1.49e+04 1.63e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.16e+00 ... (remaining 25628 not shown) Histogram of bond angle deviations from ideal: 100.19 - 107.07: 774 107.07 - 113.94: 14708 113.94 - 120.82: 10594 120.82 - 127.70: 8638 127.70 - 134.57: 154 Bond angle restraints: 34868 Sorted by residual: angle pdb=" C LEU C 213 " pdb=" N PRO C 214 " pdb=" CA PRO C 214 " ideal model delta sigma weight residual 119.84 134.57 -14.73 1.25e+00 6.40e-01 1.39e+02 angle pdb=" C THR C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.84 129.44 -9.60 1.25e+00 6.40e-01 5.90e+01 angle pdb=" N GLY C 443 " pdb=" CA GLY C 443 " pdb=" C GLY C 443 " ideal model delta sigma weight residual 113.18 126.32 -13.14 2.37e+00 1.78e-01 3.07e+01 angle pdb=" N ILE A 98 " pdb=" CA ILE A 98 " pdb=" C ILE A 98 " ideal model delta sigma weight residual 113.71 108.47 5.24 9.50e-01 1.11e+00 3.05e+01 angle pdb=" N THR C 205 " pdb=" CA THR C 205 " pdb=" C THR C 205 " ideal model delta sigma weight residual 109.81 118.79 -8.98 2.21e+00 2.05e-01 1.65e+01 ... (remaining 34863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.92: 15181 22.92 - 45.84: 861 45.84 - 68.76: 141 68.76 - 91.67: 58 91.67 - 114.59: 68 Dihedral angle restraints: 16309 sinusoidal: 7397 harmonic: 8912 Sorted by residual: dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual 93.00 177.04 -84.04 1 1.00e+01 1.00e-02 8.60e+01 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 -168.53 82.53 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS B 659 " pdb=" SG CYS B 659 " pdb=" SG CYS B 668 " pdb=" CB CYS B 668 " ideal model delta sinusoidal sigma weight residual 93.00 171.62 -78.62 1 1.00e+01 1.00e-02 7.71e+01 ... (remaining 16306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3863 0.093 - 0.186: 313 0.186 - 0.279: 11 0.279 - 0.371: 5 0.371 - 0.464: 3 Chirality restraints: 4195 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 231 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 4192 not shown) Planarity restraints: 4452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 596 " -0.046 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO A 597 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 597 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 597 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 213 " -0.039 5.00e-02 4.00e+02 5.76e-02 5.32e+00 pdb=" N PRO C 214 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 214 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 214 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 798 " -0.000 2.00e-02 2.50e+03 1.96e-02 4.80e+00 pdb=" CG ASN A 798 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 798 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 798 " -0.023 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.021 2.00e-02 2.50e+03 ... (remaining 4449 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 267 2.64 - 3.20: 21824 3.20 - 3.77: 34957 3.77 - 4.33: 47354 4.33 - 4.90: 80853 Nonbonded interactions: 185255 Sorted by model distance: nonbonded pdb=" CB THR C 205 " pdb=" CD PRO C 206 " model vdw 2.069 3.870 nonbonded pdb=" OG SER B 732 " pdb=" OG1 THR B 856 " model vdw 2.137 2.440 nonbonded pdb=" OD2 ASP C 575 " pdb=" OG1 THR C 578 " model vdw 2.157 2.440 nonbonded pdb=" NH1 ARG B 400 " pdb=" OH TYR B 498 " model vdw 2.169 2.520 nonbonded pdb=" OG1 THR A 320 " pdb=" OE1 GLU A 321 " model vdw 2.178 2.440 ... (remaining 185250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 170 or resid 184 through 206 or resid 215 throu \ gh 240 or resid 262 through 617 or resid 638 through 672 or resid 688 through 82 \ 4 or resid 843 or resid 850 through 1143 or resid 2001 through 2004)) selection = (chain 'B' and (resid 27 through 170 or resid 184 through 617 or resid 638 throu \ gh 824 or resid 843 or resid 850 through 1143 or resid 2002 through 2005)) selection = (chain 'C' and (resid 27 through 170 or resid 184 through 206 or resid 215 throu \ gh 260 or resid 262 through 824 or resid 849 through 1143 or resid 2002 through \ 2005)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.530 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 68.500 Find NCS groups from input model: 2.090 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25633 Z= 0.265 Angle : 0.714 14.731 34868 Z= 0.381 Chirality : 0.051 0.464 4195 Planarity : 0.004 0.071 4404 Dihedral : 16.614 114.593 10467 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.93 % Favored : 93.87 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 3017 helix: 1.48 (0.22), residues: 640 sheet: 0.04 (0.20), residues: 655 loop : -1.76 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.002 0.000 HIS B1061 PHE 0.025 0.001 PHE B 389 TYR 0.015 0.001 TYR B1064 ARG 0.012 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 2.954 Fit side-chains revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7422 (mp0) cc_final: 0.7190 (mp0) REVERT: A 883 TRP cc_start: 0.6987 (p90) cc_final: 0.6403 (p90) REVERT: B 315 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8055 (p90) REVERT: B 1129 ILE cc_start: 0.7724 (pt) cc_final: 0.7482 (pt) REVERT: C 418 TYR cc_start: 0.7289 (m-10) cc_final: 0.6904 (m-80) REVERT: C 452 LEU cc_start: 0.8058 (mt) cc_final: 0.6435 (mt) REVERT: C 1111 ILE cc_start: 0.8410 (tp) cc_final: 0.8186 (mt) outliers start: 7 outliers final: 1 residues processed: 198 average time/residue: 0.3579 time to fit residues: 114.2306 Evaluate side-chains 138 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain C residue 441 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 239 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 331 ASN A 752 GLN B 66 HIS C 79 ASN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25633 Z= 0.291 Angle : 0.662 10.896 34868 Z= 0.326 Chirality : 0.050 0.451 4195 Planarity : 0.004 0.059 4404 Dihedral : 13.182 99.564 5005 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.80 % Favored : 94.00 % Rotamer: Outliers : 0.93 % Allowed : 6.54 % Favored : 92.52 % 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: -0.93 (0.15), residues: 3017 helix: 1.55 (0.22), residues: 637 sheet: -0.04 (0.19), residues: 683 loop : -1.82 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.007 0.001 HIS C 204 PHE 0.027 0.002 PHE A 165 TYR 0.024 0.001 TYR B 450 ARG 0.006 0.000 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 2.731 Fit side-chains REVERT: A 139 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7604 (mt) REVERT: B 315 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7871 (p90) REVERT: B 1129 ILE cc_start: 0.8100 (pt) cc_final: 0.7880 (pt) REVERT: C 418 TYR cc_start: 0.7589 (m-10) cc_final: 0.7057 (m-80) REVERT: C 450 TYR cc_start: 0.7505 (p90) cc_final: 0.7167 (p90) REVERT: C 452 LEU cc_start: 0.7872 (mt) cc_final: 0.7507 (mt) REVERT: C 1111 ILE cc_start: 0.8387 (tp) cc_final: 0.8148 (mt) outliers start: 25 outliers final: 18 residues processed: 159 average time/residue: 0.3410 time to fit residues: 91.2884 Evaluate side-chains 153 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 351 ASN B 911 ASN C 79 ASN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25633 Z= 0.370 Angle : 0.696 12.105 34868 Z= 0.345 Chirality : 0.050 0.407 4195 Planarity : 0.005 0.058 4404 Dihedral : 11.447 101.912 5001 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.60 % Favored : 93.24 % Rotamer: Outliers : 1.87 % Allowed : 9.54 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3017 helix: 1.40 (0.21), residues: 643 sheet: -0.14 (0.20), residues: 682 loop : -1.93 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 64 HIS 0.018 0.001 HIS B 66 PHE 0.027 0.002 PHE A1118 TYR 0.024 0.002 TYR B 450 ARG 0.007 0.000 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 144 time to evaluate : 3.020 Fit side-chains REVERT: A 139 LEU cc_start: 0.7925 (mm) cc_final: 0.7708 (mt) REVERT: B 315 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7834 (p90) REVERT: C 418 TYR cc_start: 0.7747 (m-80) cc_final: 0.7066 (m-80) REVERT: C 450 TYR cc_start: 0.7524 (p90) cc_final: 0.7127 (p90) REVERT: C 452 LEU cc_start: 0.7884 (mt) cc_final: 0.7370 (mt) REVERT: C 897 MET cc_start: 0.7954 (mtp) cc_final: 0.7726 (mtm) REVERT: C 1111 ILE cc_start: 0.8449 (tp) cc_final: 0.8187 (mt) outliers start: 50 outliers final: 34 residues processed: 186 average time/residue: 0.3658 time to fit residues: 116.9386 Evaluate side-chains 170 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 278 optimal weight: 0.9980 chunk 294 optimal weight: 0.0770 chunk 145 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 ASN B 66 HIS B 999 GLN C 132 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25633 Z= 0.179 Angle : 0.604 12.863 34868 Z= 0.296 Chirality : 0.047 0.396 4195 Planarity : 0.004 0.064 4404 Dihedral : 10.281 101.816 5001 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.27 % Favored : 94.56 % Rotamer: Outliers : 1.83 % Allowed : 11.59 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3017 helix: 1.70 (0.22), residues: 643 sheet: -0.07 (0.19), residues: 685 loop : -1.75 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.004 0.001 HIS C 204 PHE 0.016 0.001 PHE A 165 TYR 0.021 0.001 TYR B 450 ARG 0.002 0.000 ARG C 643 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 148 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8279 (m) REVERT: C 330 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7186 (t) REVERT: C 418 TYR cc_start: 0.7840 (m-80) cc_final: 0.7200 (m-80) REVERT: C 450 TYR cc_start: 0.7501 (p90) cc_final: 0.7093 (p90) REVERT: C 452 LEU cc_start: 0.7845 (mt) cc_final: 0.7303 (mt) REVERT: C 1111 ILE cc_start: 0.8371 (tp) cc_final: 0.8129 (mt) outliers start: 49 outliers final: 33 residues processed: 188 average time/residue: 0.3156 time to fit residues: 101.0620 Evaluate side-chains 176 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 203 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 150 optimal weight: 0.4980 chunk 264 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25633 Z= 0.175 Angle : 0.583 12.526 34868 Z= 0.286 Chirality : 0.046 0.379 4195 Planarity : 0.004 0.067 4404 Dihedral : 9.713 100.394 4999 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.54 % Favored : 94.30 % Rotamer: Outliers : 2.09 % Allowed : 12.94 % Favored : 84.97 % 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: -0.74 (0.15), residues: 3017 helix: 1.75 (0.22), residues: 645 sheet: -0.00 (0.19), residues: 683 loop : -1.69 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.006 0.001 HIS B 66 PHE 0.019 0.001 PHE A 852 TYR 0.019 0.001 TYR B 450 ARG 0.002 0.000 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 147 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8270 (m) REVERT: C 330 THR cc_start: 0.7419 (OUTLIER) cc_final: 0.7155 (t) REVERT: C 452 LEU cc_start: 0.7832 (mt) cc_final: 0.7368 (mt) REVERT: C 1111 ILE cc_start: 0.8390 (tp) cc_final: 0.8154 (mt) outliers start: 56 outliers final: 44 residues processed: 192 average time/residue: 0.3331 time to fit residues: 108.0248 Evaluate side-chains 185 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 139 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 430 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 592 VAL Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1028 GLU Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 295 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN B 962 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25633 Z= 0.295 Angle : 0.634 11.900 34868 Z= 0.314 Chirality : 0.048 0.369 4195 Planarity : 0.004 0.071 4404 Dihedral : 9.481 100.080 4999 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.33 % Favored : 93.50 % Rotamer: Outliers : 2.51 % Allowed : 13.43 % Favored : 84.07 % 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: -0.87 (0.15), residues: 3017 helix: 1.65 (0.22), residues: 643 sheet: -0.06 (0.20), residues: 678 loop : -1.78 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.004 0.001 HIS C1085 PHE 0.023 0.002 PHE A1118 TYR 0.021 0.001 TYR C 450 ARG 0.005 0.000 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 147 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8317 (m) REVERT: B 64 TRP cc_start: 0.7736 (t60) cc_final: 0.7419 (t60) REVERT: B 108 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5802 (tp) REVERT: B 315 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7759 (p90) REVERT: B 901 TYR cc_start: 0.7606 (m-10) cc_final: 0.7166 (m-10) REVERT: C 452 LEU cc_start: 0.7792 (mt) cc_final: 0.7488 (mt) REVERT: C 1111 ILE cc_start: 0.8453 (tp) cc_final: 0.8191 (mt) outliers start: 67 outliers final: 51 residues processed: 204 average time/residue: 0.3154 time to fit residues: 109.2801 Evaluate side-chains 187 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 133 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 430 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 568 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1028 GLU Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 0.8980 chunk 33 optimal weight: 50.0000 chunk 168 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 293 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25633 Z= 0.267 Angle : 0.622 11.838 34868 Z= 0.307 Chirality : 0.047 0.366 4195 Planarity : 0.004 0.072 4404 Dihedral : 9.244 100.085 4999 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.90 % Favored : 93.93 % Rotamer: Outliers : 2.66 % Allowed : 13.91 % Favored : 83.43 % 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: -0.87 (0.15), residues: 3017 helix: 1.61 (0.22), residues: 649 sheet: 0.00 (0.20), residues: 653 loop : -1.78 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS C 204 PHE 0.023 0.001 PHE A 852 TYR 0.018 0.001 TYR B1064 ARG 0.003 0.000 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 141 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8347 (m) REVERT: B 64 TRP cc_start: 0.7757 (t60) cc_final: 0.7432 (t60) REVERT: B 108 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.5845 (tp) REVERT: B 119 ASN cc_start: 0.6806 (OUTLIER) cc_final: 0.6578 (p0) REVERT: B 266 TYR cc_start: 0.7897 (m-80) cc_final: 0.7412 (m-80) REVERT: B 901 TYR cc_start: 0.7679 (m-10) cc_final: 0.7193 (m-10) REVERT: C 330 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7125 (t) REVERT: C 452 LEU cc_start: 0.7806 (mt) cc_final: 0.7525 (mt) REVERT: C 1111 ILE cc_start: 0.8463 (tp) cc_final: 0.8186 (mt) outliers start: 71 outliers final: 56 residues processed: 201 average time/residue: 0.3247 time to fit residues: 110.5251 Evaluate side-chains 194 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 134 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 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 568 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1028 GLU Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 0.1980 chunk 186 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN B1007 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.003 0.053 25633 Z= 0.217 Angle : 0.599 11.735 34868 Z= 0.295 Chirality : 0.047 0.361 4195 Planarity : 0.004 0.073 4404 Dihedral : 8.921 99.443 4999 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.63 % Favored : 94.20 % Rotamer: Outliers : 2.62 % Allowed : 14.47 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3017 helix: 1.69 (0.22), residues: 650 sheet: 0.03 (0.20), residues: 663 loop : -1.74 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.004 0.001 HIS C 204 PHE 0.017 0.001 PHE A1118 TYR 0.017 0.001 TYR B1064 ARG 0.003 0.000 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 143 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8331 (m) REVERT: B 64 TRP cc_start: 0.7733 (t60) cc_final: 0.7418 (t60) REVERT: B 108 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5751 (tp) REVERT: B 119 ASN cc_start: 0.6825 (OUTLIER) cc_final: 0.6567 (p0) REVERT: B 266 TYR cc_start: 0.7899 (m-80) cc_final: 0.7394 (m-80) REVERT: B 315 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7841 (p90) REVERT: B 901 TYR cc_start: 0.7761 (m-10) cc_final: 0.7223 (m-10) REVERT: C 452 LEU cc_start: 0.7695 (mt) cc_final: 0.7451 (mt) REVERT: C 1111 ILE cc_start: 0.8472 (tp) cc_final: 0.8192 (mt) outliers start: 70 outliers final: 62 residues processed: 202 average time/residue: 0.3154 time to fit residues: 108.8242 Evaluate side-chains 199 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 133 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 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 568 ASP Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1028 GLU Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 273 optimal weight: 0.4980 chunk 164 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 247 optimal weight: 9.9990 chunk 259 optimal weight: 0.4980 chunk 272 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25633 Z= 0.157 Angle : 0.577 11.725 34868 Z= 0.282 Chirality : 0.046 0.358 4195 Planarity : 0.004 0.072 4404 Dihedral : 8.644 98.518 4999 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 2.43 % Allowed : 15.00 % Favored : 82.57 % 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: -0.67 (0.15), residues: 3017 helix: 1.79 (0.22), residues: 652 sheet: 0.03 (0.20), residues: 686 loop : -1.65 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.005 0.000 HIS C 204 PHE 0.036 0.001 PHE A 852 TYR 0.015 0.001 TYR C 450 ARG 0.001 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 147 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8271 (m) REVERT: B 64 TRP cc_start: 0.7686 (t60) cc_final: 0.7373 (t60) REVERT: B 108 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5783 (tp) REVERT: B 463 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6573 (ptm160) REVERT: B 901 TYR cc_start: 0.7726 (m-10) cc_final: 0.7214 (m-10) REVERT: C 418 TYR cc_start: 0.7797 (m-10) cc_final: 0.7419 (m-80) REVERT: C 452 LEU cc_start: 0.7692 (mt) cc_final: 0.7462 (mt) REVERT: C 1026 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7954 (ttp) REVERT: C 1111 ILE cc_start: 0.8414 (tp) cc_final: 0.8134 (mt) outliers start: 65 outliers final: 49 residues processed: 203 average time/residue: 0.3179 time to fit residues: 108.7002 Evaluate side-chains 194 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 141 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 463 ARG 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 617 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1028 GLU Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 1.9990 chunk 289 optimal weight: 0.7980 chunk 176 optimal weight: 0.0170 chunk 137 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 chunk 279 optimal weight: 0.3980 chunk 241 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25633 Z= 0.166 Angle : 0.582 11.625 34868 Z= 0.284 Chirality : 0.047 0.695 4195 Planarity : 0.004 0.071 4404 Dihedral : 8.436 97.768 4999 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.34 % Favored : 94.46 % Rotamer: Outliers : 2.13 % Allowed : 15.18 % Favored : 82.69 % 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: -0.62 (0.15), residues: 3017 helix: 1.81 (0.22), residues: 650 sheet: 0.06 (0.20), residues: 686 loop : -1.60 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.004 0.000 HIS C 204 PHE 0.022 0.001 PHE C1072 TYR 0.023 0.001 TYR B 450 ARG 0.002 0.000 ARG B 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6034 Ramachandran restraints generated. 3017 Oldfield, 0 Emsley, 3017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 143 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8309 (p) REVERT: B 64 TRP cc_start: 0.7686 (t60) cc_final: 0.7378 (t60) REVERT: B 108 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5773 (tp) REVERT: B 266 TYR cc_start: 0.7896 (m-80) cc_final: 0.7344 (m-80) REVERT: B 463 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6573 (ptm160) REVERT: B 901 TYR cc_start: 0.7716 (m-10) cc_final: 0.7208 (m-10) REVERT: C 418 TYR cc_start: 0.7803 (m-10) cc_final: 0.7419 (m-80) REVERT: C 452 LEU cc_start: 0.7698 (mt) cc_final: 0.7475 (mt) REVERT: C 1026 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8013 (ttp) REVERT: C 1111 ILE cc_start: 0.8411 (tp) cc_final: 0.8135 (mt) outliers start: 57 outliers final: 50 residues processed: 192 average time/residue: 0.3262 time to fit residues: 105.1790 Evaluate side-chains 194 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 140 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 463 ARG 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 617 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1143 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 911 ASN Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1028 GLU Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain C residue 1142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 248 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.167597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111066 restraints weight = 36918.680| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.67 r_work: 0.3253 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25633 Z= 0.274 Angle : 0.631 11.410 34868 Z= 0.312 Chirality : 0.049 0.675 4195 Planarity : 0.004 0.074 4404 Dihedral : 8.392 97.933 4999 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.17 % Favored : 93.64 % Rotamer: Outliers : 2.28 % Allowed : 14.96 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.80 (0.15), residues: 3017 helix: 1.61 (0.21), residues: 654 sheet: -0.03 (0.20), residues: 679 loop : -1.70 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS C 204 PHE 0.024 0.001 PHE A1118 TYR 0.024 0.001 TYR B 450 ARG 0.004 0.000 ARG C1036 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4473.68 seconds wall clock time: 83 minutes 6.06 seconds (4986.06 seconds total)