Starting phenix.real_space_refine on Thu Feb 5 08:46:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gst_51554/02_2026/9gst_51554.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gst_51554/02_2026/9gst_51554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gst_51554/02_2026/9gst_51554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gst_51554/02_2026/9gst_51554.map" model { file = "/net/cci-nas-00/data/ceres_data/9gst_51554/02_2026/9gst_51554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gst_51554/02_2026/9gst_51554.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.017 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 119 5.16 5 C 9953 2.51 5 N 2641 2.21 5 O 3220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15933 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3432 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 22, 'TRANS': 414} Chain breaks: 3 Chain: "B" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "C" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3373 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 3 Chain: "D" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 895 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain breaks: 1 Chain: "E" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3349 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 22, 'TRANS': 402} Chain breaks: 4 Chain: "F" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 938 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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: "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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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 Time building chain proxies: 3.01, per 1000 atoms: 0.19 Number of scatterers: 15933 At special positions: 0 Unit cell: (128.52, 120.12, 155.4, 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 119 16.00 O 3220 8.00 N 2641 7.00 C 9953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 Q 2 " - " BMA Q 3 " " 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 a 2 " - " BMA a 3 " " 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 f 2 " - " BMA f 3 " " 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 A 601 " - " ASN A 339 " " NAG A 602 " - " ASN A 363 " " NAG A 603 " - " ASN A 392 " " NAG A 604 " - " ASN A 133 " " NAG A 605 " - " ASN A 137 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 618 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 363 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 355 " " NAG E 606 " - " ASN E 363 " " NAG E 607 " - " ASN E 392 " " NAG E 608 " - " ASN E 133 " " NAG E 609 " - " ASN E 295 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 301 " " NAG M 1 " - " ASN A 332 " " NAG N 1 " - " ASN A 448 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 386 " " NAG T 1 " - " ASN A 197 " " NAG U 1 " - " ASN C 197 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 160 " " NAG X 1 " - " ASN C 276 " " NAG Y 1 " - " ASN C 386 " " NAG Z 1 " - " ASN C 448 " " NAG a 1 " - " ASN C 262 " " NAG b 1 " - " ASN C 301 " " NAG c 1 " - " ASN C 332 " " NAG d 1 " - " ASN E 156 " " NAG e 1 " - " ASN E 448 " " NAG f 1 " - " ASN E 262 " " NAG g 1 " - " ASN E 276 " " NAG h 1 " - " ASN E 332 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 160 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 638.5 milliseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3478 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 29 sheets defined 21.9% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.166A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.622A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.617A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.734A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.758A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 527 removed outlier: 3.816A pdb=" N ALA B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 537 removed outlier: 3.774A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 5.079A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.960A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.733A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.780A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.600A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.512A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.115A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.716A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.679A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 643 Processing helix chain 'D' and resid 644 through 646 No H-bonds generated for 'chain 'D' and resid 644 through 646' Processing helix chain 'D' and resid 647 through 652 Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.041A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.520A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.635A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.924A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.593A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.602A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 538 through 543' Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.763A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 625 removed outlier: 3.844A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 639 through 649 Processing helix chain 'F' and resid 650 through 658 Processing helix chain 'H' and resid 61 through 65 removed outlier: 5.553A pdb=" N ASN H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 86 removed outlier: 4.487A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N LYS A 487 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ASP A 47 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL A 489 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N TRP A 45 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ILE A 491 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.766A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.339A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.260A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.170A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.102A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.053A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.170A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 312 removed outlier: 6.604A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.040A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.895A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.631A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.610A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.403A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.609A pdb=" N PHE C 288 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.388A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.256A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 35 through 47 removed outlier: 8.573A pdb=" N VAL E 38 " --> pdb=" O PRO E 498 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N TYR E 40 " --> pdb=" O VAL E 496 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N VAL E 496 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL E 42 " --> pdb=" O LEU E 494 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU E 494 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL E 44 " --> pdb=" O GLU E 492 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.566A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC2, first strand: chain 'E' and resid 202 through 203 removed outlier: 7.090A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 261 removed outlier: 5.633A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 274 removed outlier: 4.720A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 302 through 312 removed outlier: 5.869A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.467A pdb=" N TRP H 34 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.599A pdb=" N CYS H 95 " --> pdb=" O TRP H 113 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TRP H 113 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG H 97 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AC9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.503A pdb=" N TRP L 34 " --> pdb=" O ILE L 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 12 555 hydrogen bonds defined for protein. 1491 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: 2.56 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3709 1.33 - 1.46: 4632 1.46 - 1.58: 7737 1.58 - 1.71: 0 1.71 - 1.84: 162 Bond restraints: 16240 Sorted by residual: bond pdb=" N ALA H 100 " pdb=" CA ALA H 100 " ideal model delta sigma weight residual 1.458 1.377 0.080 1.16e-02 7.43e+03 4.76e+01 bond pdb=" CA SER H 103 " pdb=" C SER H 103 " ideal model delta sigma weight residual 1.520 1.494 0.026 4.80e-03 4.34e+04 2.93e+01 bond pdb=" CA MET B 535 " pdb=" CB MET B 535 " ideal model delta sigma weight residual 1.530 1.446 0.084 1.57e-02 4.06e+03 2.84e+01 bond pdb=" CA LEU D 645 " pdb=" C LEU D 645 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.34e-02 5.57e+03 2.73e+01 bond pdb=" CA ALA H 100 " pdb=" C ALA H 100 " ideal model delta sigma weight residual 1.520 1.464 0.057 1.20e-02 6.94e+03 2.24e+01 ... (remaining 16235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 21371 2.33 - 4.65: 592 4.65 - 6.98: 69 6.98 - 9.30: 10 9.30 - 11.63: 5 Bond angle restraints: 22047 Sorted by residual: angle pdb=" N ASP H 104 " pdb=" CA ASP H 104 " pdb=" C ASP H 104 " ideal model delta sigma weight residual 113.41 103.88 9.53 1.22e+00 6.72e-01 6.10e+01 angle pdb=" N ARG C 480 " pdb=" CA ARG C 480 " pdb=" C ARG C 480 " ideal model delta sigma weight residual 111.69 102.36 9.33 1.23e+00 6.61e-01 5.76e+01 angle pdb=" N MET A 475 " pdb=" CA MET A 475 " pdb=" C MET A 475 " ideal model delta sigma weight residual 113.30 104.89 8.41 1.34e+00 5.57e-01 3.94e+01 angle pdb=" N ARG H 101 " pdb=" CA ARG H 101 " pdb=" C ARG H 101 " ideal model delta sigma weight residual 109.85 100.06 9.79 1.58e+00 4.01e-01 3.84e+01 angle pdb=" N ALA F 532 " pdb=" CA ALA F 532 " pdb=" C ALA F 532 " ideal model delta sigma weight residual 111.82 105.41 6.41 1.16e+00 7.43e-01 3.05e+01 ... (remaining 22042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 9934 23.90 - 47.79: 835 47.79 - 71.69: 113 71.69 - 95.59: 41 95.59 - 119.48: 58 Dihedral angle restraints: 10981 sinusoidal: 5604 harmonic: 5377 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 -179.26 -87.74 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -0.38 -85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -5.41 -80.59 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 10978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2588 0.101 - 0.202: 155 0.202 - 0.303: 8 0.303 - 0.404: 2 0.404 - 0.505: 1 Chirality restraints: 2754 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.29e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 160 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 88 " 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 3.77e+00 ... (remaining 2751 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " 0.336 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG T 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.090 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " -0.519 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 704 " -0.316 2.00e-02 2.50e+03 2.72e-01 9.25e+02 pdb=" C7 NAG B 704 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B 704 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG B 704 " 0.481 2.00e-02 2.50e+03 pdb=" O7 NAG B 704 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.246 2.00e-02 2.50e+03 2.04e-01 5.18e+02 pdb=" C7 NAG G 2 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.336 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.016 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 693 2.71 - 3.25: 15225 3.25 - 3.80: 25231 3.80 - 4.35: 31379 4.35 - 4.90: 53344 Nonbonded interactions: 125872 Sorted by model distance: nonbonded pdb=" OE1 GLU C 275 " pdb=" NZ LYS C 282 " model vdw 2.156 3.120 nonbonded pdb=" ND2 ASN A 195 " pdb=" O SER A 199 " model vdw 2.167 3.120 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.173 3.040 nonbonded pdb=" ND1 HIS C 249 " pdb=" OH TYR C 486 " model vdw 2.250 3.120 nonbonded pdb=" OG SER A 264 " pdb=" OE1 GLU A 482 " model vdw 2.251 3.040 ... (remaining 125867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 34 through 58 or resid 74 through 184 or resid 189 through \ 398 or resid 412 through 457 or resid 464 through 605)) selection = (chain 'C' and (resid 34 through 58 or resid 74 through 457 or resid 464 through \ 605)) selection = (chain 'E' and (resid 34 through 184 or resid 189 through 398 or resid 412 throu \ gh 605)) } ncs_group { reference = (chain 'B' and (resid 522 through 654 or resid 703 through 704)) selection = (chain 'D' and (resid 522 through 541 or resid 568 through 702)) selection = (chain 'F' and (resid 522 through 541 or resid 568 through 654 or resid 701 thro \ ugh 702)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' 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 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'Q' selection = chain 'a' } 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.780 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.008 0.084 16371 Z= 0.408 Angle : 0.929 12.106 22402 Z= 0.471 Chirality : 0.055 0.505 2754 Planarity : 0.010 0.292 2679 Dihedral : 18.654 119.483 7389 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.80 % Favored : 93.04 % Rotamer: Outliers : 1.09 % Allowed : 23.03 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1824 helix: -0.65 (0.27), residues: 383 sheet: 0.22 (0.22), residues: 520 loop : -1.20 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 166 TYR 0.021 0.002 TYR D 638 PHE 0.016 0.002 PHE A 361 TRP 0.030 0.002 TRP H 47 HIS 0.008 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00755 (16240) covalent geometry : angle 0.88455 (22047) SS BOND : bond 0.00393 ( 38) SS BOND : angle 1.35880 ( 76) hydrogen bonds : bond 0.12601 ( 532) hydrogen bonds : angle 6.63812 ( 1491) link_ALPHA1-2 : bond 0.00638 ( 1) link_ALPHA1-2 : angle 1.77177 ( 3) link_ALPHA1-3 : bond 0.00417 ( 3) link_ALPHA1-3 : angle 1.65445 ( 9) link_ALPHA1-6 : bond 0.00349 ( 1) link_ALPHA1-6 : angle 1.83205 ( 3) link_BETA1-4 : bond 0.00496 ( 31) link_BETA1-4 : angle 1.83365 ( 93) link_NAG-ASN : bond 0.00603 ( 57) link_NAG-ASN : angle 3.05866 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 580 VAL cc_start: 0.9216 (t) cc_final: 0.8708 (t) REVERT: H 65 ASN cc_start: 0.8419 (p0) cc_final: 0.8197 (p0) REVERT: L 27 MET cc_start: 0.7199 (ttt) cc_final: 0.6979 (tmm) outliers start: 18 outliers final: 2 residues processed: 256 average time/residue: 0.1337 time to fit residues: 48.9167 Evaluate side-chains 162 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain H residue 104 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 577 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.053157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040148 restraints weight = 72244.757| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 4.38 r_work: 0.2664 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16371 Z= 0.193 Angle : 0.758 11.884 22402 Z= 0.358 Chirality : 0.047 0.283 2754 Planarity : 0.005 0.055 2679 Dihedral : 12.846 107.860 3923 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.57 % Rotamer: Outliers : 3.58 % Allowed : 20.90 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1824 helix: -0.11 (0.28), residues: 373 sheet: 0.13 (0.22), residues: 509 loop : -0.95 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 60 TYR 0.010 0.001 TYR A 318 PHE 0.018 0.002 PHE C 382 TRP 0.016 0.001 TRP H 47 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00425 (16240) covalent geometry : angle 0.71453 (22047) SS BOND : bond 0.00344 ( 38) SS BOND : angle 1.06381 ( 76) hydrogen bonds : bond 0.04064 ( 532) hydrogen bonds : angle 5.50393 ( 1491) link_ALPHA1-2 : bond 0.00865 ( 1) link_ALPHA1-2 : angle 1.35174 ( 3) link_ALPHA1-3 : bond 0.00927 ( 3) link_ALPHA1-3 : angle 2.52103 ( 9) link_ALPHA1-6 : bond 0.00309 ( 1) link_ALPHA1-6 : angle 3.27925 ( 3) link_BETA1-4 : bond 0.00387 ( 31) link_BETA1-4 : angle 1.68854 ( 93) link_NAG-ASN : bond 0.00436 ( 57) link_NAG-ASN : angle 2.62250 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 543 ASN cc_start: 0.8911 (t0) cc_final: 0.8626 (t0) REVERT: E 53 PHE cc_start: 0.7563 (p90) cc_final: 0.7362 (p90) REVERT: E 87 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8811 (mp0) REVERT: E 102 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: F 543 ASN cc_start: 0.9068 (m110) cc_final: 0.8725 (p0) REVERT: F 571 TRP cc_start: 0.8464 (m-90) cc_final: 0.7987 (m-90) REVERT: F 648 GLU cc_start: 0.9163 (pp20) cc_final: 0.8838 (pp20) REVERT: F 657 GLU cc_start: 0.9110 (tt0) cc_final: 0.8816 (pt0) REVERT: H 4 LEU cc_start: 0.8868 (mt) cc_final: 0.8454 (mp) REVERT: L 27 MET cc_start: 0.7292 (ttt) cc_final: 0.6443 (tmm) REVERT: L 94 TYR cc_start: 0.9141 (m-10) cc_final: 0.8788 (m-10) REVERT: L 95 GLU cc_start: 0.8737 (mp0) cc_final: 0.8370 (mp0) outliers start: 59 outliers final: 24 residues processed: 225 average time/residue: 0.1133 time to fit residues: 38.6357 Evaluate side-chains 179 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 142 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN A 478 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 183 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.052189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.039138 restraints weight = 73520.583| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 4.39 r_work: 0.2655 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16371 Z= 0.221 Angle : 0.713 10.715 22402 Z= 0.340 Chirality : 0.045 0.275 2754 Planarity : 0.004 0.055 2679 Dihedral : 10.817 105.942 3921 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.40 % Allowed : 21.32 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.20), residues: 1824 helix: -0.14 (0.27), residues: 383 sheet: 0.11 (0.22), residues: 529 loop : -0.91 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 542 TYR 0.013 0.001 TYR F 643 PHE 0.016 0.001 PHE C 382 TRP 0.017 0.001 TRP A 112 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00493 (16240) covalent geometry : angle 0.66851 (22047) SS BOND : bond 0.00378 ( 38) SS BOND : angle 1.14017 ( 76) hydrogen bonds : bond 0.03957 ( 532) hydrogen bonds : angle 5.35707 ( 1491) link_ALPHA1-2 : bond 0.00775 ( 1) link_ALPHA1-2 : angle 1.46301 ( 3) link_ALPHA1-3 : bond 0.00982 ( 3) link_ALPHA1-3 : angle 1.64844 ( 9) link_ALPHA1-6 : bond 0.00494 ( 1) link_ALPHA1-6 : angle 2.70891 ( 3) link_BETA1-4 : bond 0.00270 ( 31) link_BETA1-4 : angle 1.48300 ( 93) link_NAG-ASN : bond 0.00575 ( 57) link_NAG-ASN : angle 2.63301 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 155 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 655 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8256 (mmmm) REVERT: C 150 MET cc_start: 0.8993 (tpp) cc_final: 0.8768 (tpp) REVERT: D 543 ASN cc_start: 0.9067 (t0) cc_final: 0.8620 (t0) REVERT: E 87 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8817 (mp0) REVERT: E 99 ASN cc_start: 0.8653 (OUTLIER) cc_final: 0.8062 (t0) REVERT: E 102 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: F 543 ASN cc_start: 0.9098 (m110) cc_final: 0.8784 (p0) REVERT: F 571 TRP cc_start: 0.8509 (m-90) cc_final: 0.8047 (m-90) REVERT: F 584 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8866 (tm-30) REVERT: F 588 ARG cc_start: 0.9275 (ttm170) cc_final: 0.9013 (ttp-110) REVERT: H 4 LEU cc_start: 0.8859 (mt) cc_final: 0.8334 (mp) REVERT: H 78 MET cc_start: 0.8605 (ptm) cc_final: 0.8272 (ptt) REVERT: L 27 MET cc_start: 0.7134 (ttt) cc_final: 0.6326 (tmm) REVERT: L 84 ASP cc_start: 0.7533 (t0) cc_final: 0.7241 (t0) REVERT: L 94 TYR cc_start: 0.9224 (m-10) cc_final: 0.8906 (m-10) REVERT: L 95 GLU cc_start: 0.8782 (mp0) cc_final: 0.8430 (mp0) outliers start: 56 outliers final: 34 residues processed: 204 average time/residue: 0.1211 time to fit residues: 37.1718 Evaluate side-chains 182 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 125 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN E 478 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.052313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.039123 restraints weight = 72493.495| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 4.43 r_work: 0.2658 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16371 Z= 0.193 Angle : 0.684 9.427 22402 Z= 0.326 Chirality : 0.045 0.256 2754 Planarity : 0.004 0.053 2679 Dihedral : 9.738 96.399 3921 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.83 % Allowed : 21.14 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1824 helix: 0.05 (0.27), residues: 382 sheet: 0.12 (0.22), residues: 530 loop : -0.88 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 41 TYR 0.010 0.001 TYR F 638 PHE 0.014 0.001 PHE C 382 TRP 0.015 0.001 TRP A 112 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00432 (16240) covalent geometry : angle 0.64521 (22047) SS BOND : bond 0.00318 ( 38) SS BOND : angle 0.90342 ( 76) hydrogen bonds : bond 0.03684 ( 532) hydrogen bonds : angle 5.18215 ( 1491) link_ALPHA1-2 : bond 0.00733 ( 1) link_ALPHA1-2 : angle 1.52594 ( 3) link_ALPHA1-3 : bond 0.00999 ( 3) link_ALPHA1-3 : angle 1.67373 ( 9) link_ALPHA1-6 : bond 0.00776 ( 1) link_ALPHA1-6 : angle 2.92081 ( 3) link_BETA1-4 : bond 0.00280 ( 31) link_BETA1-4 : angle 1.48162 ( 93) link_NAG-ASN : bond 0.00362 ( 57) link_NAG-ASN : angle 2.39817 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 160 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: A 428 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8727 (mp10) REVERT: D 530 MET cc_start: 0.8990 (mtp) cc_final: 0.8743 (mtm) REVERT: D 543 ASN cc_start: 0.9109 (t0) cc_final: 0.8705 (t0) REVERT: E 87 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8908 (mp0) REVERT: E 99 ASN cc_start: 0.8622 (p0) cc_final: 0.8111 (t0) REVERT: E 102 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: E 426 MET cc_start: 0.9035 (mmm) cc_final: 0.8601 (mmm) REVERT: F 543 ASN cc_start: 0.9078 (m110) cc_final: 0.8767 (p0) REVERT: F 571 TRP cc_start: 0.8565 (m-90) cc_final: 0.8071 (m-90) REVERT: F 584 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8936 (tm-30) REVERT: F 588 ARG cc_start: 0.9261 (ttm170) cc_final: 0.8875 (ttp-110) REVERT: H 4 LEU cc_start: 0.8814 (mt) cc_final: 0.8366 (mp) REVERT: H 78 MET cc_start: 0.8762 (ptm) cc_final: 0.8252 (ptt) REVERT: L 27 MET cc_start: 0.6950 (ttt) cc_final: 0.6251 (tmm) REVERT: L 84 ASP cc_start: 0.7529 (t0) cc_final: 0.7215 (t0) REVERT: L 94 TYR cc_start: 0.9235 (m-10) cc_final: 0.8894 (m-10) REVERT: L 95 GLU cc_start: 0.8786 (mp0) cc_final: 0.8414 (mp0) outliers start: 63 outliers final: 39 residues processed: 212 average time/residue: 0.1098 time to fit residues: 35.5567 Evaluate side-chains 194 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 97 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN L 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.038127 restraints weight = 73032.205| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 4.38 r_work: 0.2625 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16371 Z= 0.264 Angle : 0.721 9.803 22402 Z= 0.342 Chirality : 0.045 0.259 2754 Planarity : 0.004 0.052 2679 Dihedral : 9.052 90.010 3921 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.89 % Allowed : 21.81 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.20), residues: 1824 helix: -0.10 (0.27), residues: 395 sheet: 0.10 (0.22), residues: 529 loop : -0.93 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 542 TYR 0.010 0.001 TYR F 638 PHE 0.015 0.001 PHE C 382 TRP 0.019 0.001 TRP C 112 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00589 (16240) covalent geometry : angle 0.68032 (22047) SS BOND : bond 0.00374 ( 38) SS BOND : angle 0.97141 ( 76) hydrogen bonds : bond 0.03776 ( 532) hydrogen bonds : angle 5.21198 ( 1491) link_ALPHA1-2 : bond 0.00667 ( 1) link_ALPHA1-2 : angle 1.49602 ( 3) link_ALPHA1-3 : bond 0.00853 ( 3) link_ALPHA1-3 : angle 1.67085 ( 9) link_ALPHA1-6 : bond 0.00811 ( 1) link_ALPHA1-6 : angle 3.29214 ( 3) link_BETA1-4 : bond 0.00248 ( 31) link_BETA1-4 : angle 1.55507 ( 93) link_NAG-ASN : bond 0.00480 ( 57) link_NAG-ASN : angle 2.50266 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: B 588 ARG cc_start: 0.9353 (tpt170) cc_final: 0.9126 (tpt170) REVERT: B 655 LYS cc_start: 0.8751 (mmtp) cc_final: 0.8205 (mmmm) REVERT: C 447 SER cc_start: 0.9241 (OUTLIER) cc_final: 0.8747 (m) REVERT: D 530 MET cc_start: 0.8971 (mtp) cc_final: 0.8529 (mtm) REVERT: D 543 ASN cc_start: 0.9107 (t0) cc_final: 0.8746 (t0) REVERT: E 87 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8913 (mp0) REVERT: E 102 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: E 426 MET cc_start: 0.9080 (mmm) cc_final: 0.8856 (mmm) REVERT: F 543 ASN cc_start: 0.9135 (m110) cc_final: 0.8844 (p0) REVERT: F 571 TRP cc_start: 0.8596 (m-90) cc_final: 0.8080 (m-90) REVERT: F 584 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8795 (tm-30) REVERT: F 588 ARG cc_start: 0.9256 (ttm170) cc_final: 0.8940 (ttm110) REVERT: H 4 LEU cc_start: 0.8838 (mt) cc_final: 0.8377 (mp) REVERT: H 78 MET cc_start: 0.8739 (ptm) cc_final: 0.8221 (ptt) REVERT: L 26 TYR cc_start: 0.8742 (m-80) cc_final: 0.8231 (m-10) REVERT: L 27 MET cc_start: 0.7098 (ttt) cc_final: 0.6437 (tmm) REVERT: L 41 ARG cc_start: 0.6449 (mpp80) cc_final: 0.6183 (mpp80) REVERT: L 84 ASP cc_start: 0.7509 (t0) cc_final: 0.7193 (t0) REVERT: L 94 TYR cc_start: 0.9269 (m-10) cc_final: 0.8641 (m-10) REVERT: L 95 GLU cc_start: 0.8822 (mp0) cc_final: 0.8449 (mp0) outliers start: 64 outliers final: 42 residues processed: 207 average time/residue: 0.1133 time to fit residues: 35.5214 Evaluate side-chains 193 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 144 optimal weight: 0.7980 chunk 43 optimal weight: 0.0040 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN D 652 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN L 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.052407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.039262 restraints weight = 72247.945| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 4.42 r_work: 0.2668 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16371 Z= 0.132 Angle : 0.655 11.031 22402 Z= 0.311 Chirality : 0.045 0.241 2754 Planarity : 0.004 0.052 2679 Dihedral : 8.197 82.281 3921 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 3.28 % Allowed : 22.90 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1824 helix: 0.15 (0.27), residues: 384 sheet: 0.13 (0.22), residues: 531 loop : -0.74 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 542 TYR 0.008 0.001 TYR C 191 PHE 0.019 0.001 PHE E 53 TRP 0.016 0.001 TRP C 112 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00294 (16240) covalent geometry : angle 0.61911 (22047) SS BOND : bond 0.00251 ( 38) SS BOND : angle 0.77000 ( 76) hydrogen bonds : bond 0.03356 ( 532) hydrogen bonds : angle 5.01004 ( 1491) link_ALPHA1-2 : bond 0.00696 ( 1) link_ALPHA1-2 : angle 1.85836 ( 3) link_ALPHA1-3 : bond 0.01030 ( 3) link_ALPHA1-3 : angle 1.32671 ( 9) link_ALPHA1-6 : bond 0.01131 ( 1) link_ALPHA1-6 : angle 2.90674 ( 3) link_BETA1-4 : bond 0.00375 ( 31) link_BETA1-4 : angle 1.40687 ( 93) link_NAG-ASN : bond 0.00361 ( 57) link_NAG-ASN : angle 2.26600 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: B 654 GLU cc_start: 0.9270 (tp30) cc_final: 0.8919 (tt0) REVERT: D 530 MET cc_start: 0.8911 (mtp) cc_final: 0.8584 (mtm) REVERT: D 543 ASN cc_start: 0.9077 (t0) cc_final: 0.8752 (t0) REVERT: E 87 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8908 (mp0) REVERT: E 99 ASN cc_start: 0.8625 (p0) cc_final: 0.8420 (t0) REVERT: E 426 MET cc_start: 0.9060 (mmm) cc_final: 0.8783 (mmm) REVERT: F 542 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.7705 (mtm-85) REVERT: F 543 ASN cc_start: 0.9103 (m110) cc_final: 0.8816 (p0) REVERT: F 574 LYS cc_start: 0.9370 (ttpt) cc_final: 0.8947 (ptmt) REVERT: F 584 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8734 (tm-30) REVERT: F 588 ARG cc_start: 0.9232 (ttm170) cc_final: 0.8884 (ttm110) REVERT: F 655 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8608 (pttt) REVERT: H 4 LEU cc_start: 0.8855 (mt) cc_final: 0.8403 (mp) REVERT: H 78 MET cc_start: 0.8692 (ptm) cc_final: 0.8250 (ptt) REVERT: L 26 TYR cc_start: 0.8751 (m-80) cc_final: 0.8254 (m-10) REVERT: L 27 MET cc_start: 0.7096 (ttt) cc_final: 0.6406 (tmm) REVERT: L 84 ASP cc_start: 0.7528 (t0) cc_final: 0.7202 (t0) REVERT: L 94 TYR cc_start: 0.9254 (m-10) cc_final: 0.8622 (m-10) REVERT: L 95 GLU cc_start: 0.8779 (mp0) cc_final: 0.8374 (mp0) outliers start: 54 outliers final: 35 residues processed: 204 average time/residue: 0.1253 time to fit residues: 38.3660 Evaluate side-chains 191 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 79 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.051061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.037956 restraints weight = 72757.092| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.38 r_work: 0.2621 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16371 Z= 0.253 Angle : 0.718 11.645 22402 Z= 0.340 Chirality : 0.045 0.274 2754 Planarity : 0.004 0.051 2679 Dihedral : 7.677 76.064 3921 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 3.58 % Allowed : 22.60 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1824 helix: -0.02 (0.27), residues: 394 sheet: 0.12 (0.22), residues: 530 loop : -0.83 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 585 TYR 0.009 0.001 TYR F 638 PHE 0.015 0.001 PHE C 382 TRP 0.018 0.001 TRP C 112 HIS 0.004 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00567 (16240) covalent geometry : angle 0.67663 (22047) SS BOND : bond 0.00387 ( 38) SS BOND : angle 0.94065 ( 76) hydrogen bonds : bond 0.03730 ( 532) hydrogen bonds : angle 5.12292 ( 1491) link_ALPHA1-2 : bond 0.00639 ( 1) link_ALPHA1-2 : angle 1.55216 ( 3) link_ALPHA1-3 : bond 0.00758 ( 3) link_ALPHA1-3 : angle 1.56227 ( 9) link_ALPHA1-6 : bond 0.01335 ( 1) link_ALPHA1-6 : angle 3.36156 ( 3) link_BETA1-4 : bond 0.00241 ( 31) link_BETA1-4 : angle 1.56241 ( 93) link_NAG-ASN : bond 0.00462 ( 57) link_NAG-ASN : angle 2.54899 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: A 116 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9324 (mp) REVERT: A 492 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: B 654 GLU cc_start: 0.9270 (tp30) cc_final: 0.8726 (tm-30) REVERT: D 530 MET cc_start: 0.8976 (mtp) cc_final: 0.8695 (mtm) REVERT: D 543 ASN cc_start: 0.9091 (t0) cc_final: 0.8795 (t0) REVERT: E 87 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8932 (mp0) REVERT: E 102 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8586 (mp0) REVERT: E 426 MET cc_start: 0.9120 (mmm) cc_final: 0.8850 (mmm) REVERT: F 535 MET cc_start: 0.9517 (mtm) cc_final: 0.9259 (mtm) REVERT: F 542 ARG cc_start: 0.8783 (mtm-85) cc_final: 0.7759 (mtm-85) REVERT: F 543 ASN cc_start: 0.9150 (m110) cc_final: 0.8822 (p0) REVERT: F 571 TRP cc_start: 0.8548 (m-90) cc_final: 0.8113 (m-90) REVERT: F 584 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8691 (tm-30) REVERT: F 588 ARG cc_start: 0.9217 (ttm170) cc_final: 0.8925 (ttm170) REVERT: F 634 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8510 (pp20) REVERT: H 4 LEU cc_start: 0.8876 (mt) cc_final: 0.8422 (mp) REVERT: H 78 MET cc_start: 0.8771 (ptm) cc_final: 0.8296 (ptt) REVERT: L 26 TYR cc_start: 0.8824 (m-80) cc_final: 0.8341 (m-10) REVERT: L 27 MET cc_start: 0.7195 (ttt) cc_final: 0.6584 (tmm) REVERT: L 82 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8300 (mm-30) REVERT: L 84 ASP cc_start: 0.7519 (t0) cc_final: 0.7202 (t0) REVERT: L 95 GLU cc_start: 0.8844 (mp0) cc_final: 0.8448 (mp0) outliers start: 59 outliers final: 39 residues processed: 200 average time/residue: 0.1071 time to fit residues: 32.5201 Evaluate side-chains 188 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 88 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 chunk 162 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 173 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN E 348 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.052495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039444 restraints weight = 72023.594| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 4.40 r_work: 0.2674 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16371 Z= 0.120 Angle : 0.658 10.618 22402 Z= 0.315 Chirality : 0.044 0.248 2754 Planarity : 0.004 0.051 2679 Dihedral : 7.045 70.214 3921 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.23 % Rotamer: Outliers : 3.22 % Allowed : 23.39 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1824 helix: 0.11 (0.27), residues: 388 sheet: 0.10 (0.22), residues: 542 loop : -0.70 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.009 0.001 TYR E 217 PHE 0.021 0.001 PHE E 53 TRP 0.016 0.001 TRP C 112 HIS 0.003 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00269 (16240) covalent geometry : angle 0.61915 (22047) SS BOND : bond 0.00240 ( 38) SS BOND : angle 1.39233 ( 76) hydrogen bonds : bond 0.03322 ( 532) hydrogen bonds : angle 4.97430 ( 1491) link_ALPHA1-2 : bond 0.00657 ( 1) link_ALPHA1-2 : angle 1.86672 ( 3) link_ALPHA1-3 : bond 0.00895 ( 3) link_ALPHA1-3 : angle 1.24513 ( 9) link_ALPHA1-6 : bond 0.01438 ( 1) link_ALPHA1-6 : angle 2.29245 ( 3) link_BETA1-4 : bond 0.00398 ( 31) link_BETA1-4 : angle 1.39287 ( 93) link_NAG-ASN : bond 0.00321 ( 57) link_NAG-ASN : angle 2.27310 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: A 428 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8882 (mp10) REVERT: A 492 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8589 (mp0) REVERT: B 654 GLU cc_start: 0.9243 (tp30) cc_final: 0.8951 (tm-30) REVERT: C 447 SER cc_start: 0.9184 (OUTLIER) cc_final: 0.8778 (m) REVERT: D 530 MET cc_start: 0.8858 (mtp) cc_final: 0.8566 (mtm) REVERT: D 543 ASN cc_start: 0.9073 (t0) cc_final: 0.8804 (t0) REVERT: D 571 TRP cc_start: 0.7800 (m100) cc_final: 0.7548 (m-10) REVERT: E 87 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8941 (mp0) REVERT: E 99 ASN cc_start: 0.8643 (p0) cc_final: 0.8191 (t0) REVERT: E 102 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: E 426 MET cc_start: 0.9049 (mmm) cc_final: 0.8771 (mmm) REVERT: F 535 MET cc_start: 0.9498 (mtm) cc_final: 0.9219 (mtm) REVERT: F 543 ASN cc_start: 0.9118 (m110) cc_final: 0.8826 (p0) REVERT: F 574 LYS cc_start: 0.9360 (ttpt) cc_final: 0.8964 (ptmt) REVERT: F 584 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8674 (tm-30) REVERT: F 588 ARG cc_start: 0.9212 (ttm170) cc_final: 0.8868 (ttm110) REVERT: H 4 LEU cc_start: 0.8932 (mt) cc_final: 0.8497 (mp) REVERT: H 78 MET cc_start: 0.8725 (ptm) cc_final: 0.8282 (ptt) REVERT: L 26 TYR cc_start: 0.8805 (m-80) cc_final: 0.8309 (m-10) REVERT: L 27 MET cc_start: 0.7161 (ttt) cc_final: 0.6564 (tmm) REVERT: L 82 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8242 (mm-30) REVERT: L 84 ASP cc_start: 0.7532 (t0) cc_final: 0.7203 (t0) REVERT: L 94 TYR cc_start: 0.9205 (m-10) cc_final: 0.8632 (m-10) REVERT: L 95 GLU cc_start: 0.8778 (mp0) cc_final: 0.8362 (mp0) outliers start: 53 outliers final: 38 residues processed: 199 average time/residue: 0.1152 time to fit residues: 34.8222 Evaluate side-chains 193 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN D 577 GLN D 651 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.038577 restraints weight = 73268.212| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 4.43 r_work: 0.2637 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16371 Z= 0.203 Angle : 0.682 9.682 22402 Z= 0.326 Chirality : 0.045 0.271 2754 Planarity : 0.004 0.051 2679 Dihedral : 6.790 64.704 3921 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 2.86 % Allowed : 23.75 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1824 helix: 0.09 (0.28), residues: 385 sheet: 0.14 (0.22), residues: 534 loop : -0.71 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 542 TYR 0.012 0.001 TYR E 217 PHE 0.014 0.001 PHE E 53 TRP 0.023 0.001 TRP F 571 HIS 0.003 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00460 (16240) covalent geometry : angle 0.64171 (22047) SS BOND : bond 0.00335 ( 38) SS BOND : angle 1.17303 ( 76) hydrogen bonds : bond 0.03476 ( 532) hydrogen bonds : angle 4.99312 ( 1491) link_ALPHA1-2 : bond 0.00620 ( 1) link_ALPHA1-2 : angle 1.64749 ( 3) link_ALPHA1-3 : bond 0.00723 ( 3) link_ALPHA1-3 : angle 1.43664 ( 9) link_ALPHA1-6 : bond 0.01589 ( 1) link_ALPHA1-6 : angle 2.10699 ( 3) link_BETA1-4 : bond 0.00295 ( 31) link_BETA1-4 : angle 1.47609 ( 93) link_NAG-ASN : bond 0.00373 ( 57) link_NAG-ASN : angle 2.41565 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: A 428 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8936 (mp10) REVERT: A 492 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8546 (mp0) REVERT: B 654 GLU cc_start: 0.9230 (tp30) cc_final: 0.8945 (tm-30) REVERT: C 447 SER cc_start: 0.9247 (OUTLIER) cc_final: 0.8770 (m) REVERT: D 530 MET cc_start: 0.8878 (mtp) cc_final: 0.8650 (mtp) REVERT: D 543 ASN cc_start: 0.9102 (t0) cc_final: 0.8840 (t0) REVERT: D 571 TRP cc_start: 0.7878 (m100) cc_final: 0.7551 (m-10) REVERT: E 87 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9001 (mp0) REVERT: E 102 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: E 426 MET cc_start: 0.9089 (mmm) cc_final: 0.8828 (mmm) REVERT: F 535 MET cc_start: 0.9501 (mtm) cc_final: 0.9242 (mtm) REVERT: F 543 ASN cc_start: 0.9159 (m110) cc_final: 0.8829 (p0) REVERT: F 574 LYS cc_start: 0.9343 (ttpt) cc_final: 0.8962 (ptmt) REVERT: F 584 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8596 (tm-30) REVERT: F 588 ARG cc_start: 0.9217 (ttm170) cc_final: 0.8840 (ttp-110) REVERT: F 648 GLU cc_start: 0.9215 (tp30) cc_final: 0.8938 (tp30) REVERT: H 4 LEU cc_start: 0.8924 (mt) cc_final: 0.8481 (mp) REVERT: H 78 MET cc_start: 0.8775 (ptm) cc_final: 0.8312 (ptt) REVERT: L 26 TYR cc_start: 0.8846 (m-80) cc_final: 0.8359 (m-10) REVERT: L 27 MET cc_start: 0.7243 (ttt) cc_final: 0.6636 (tmm) REVERT: L 82 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8237 (mm-30) REVERT: L 84 ASP cc_start: 0.7529 (t0) cc_final: 0.7216 (t0) REVERT: L 94 TYR cc_start: 0.9235 (m-10) cc_final: 0.8691 (m-10) REVERT: L 95 GLU cc_start: 0.8847 (mp0) cc_final: 0.8434 (mp0) outliers start: 47 outliers final: 37 residues processed: 191 average time/residue: 0.1198 time to fit residues: 34.7953 Evaluate side-chains 188 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 51 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.050942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.037847 restraints weight = 72883.256| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 4.39 r_work: 0.2619 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 16371 Z= 0.261 Angle : 0.715 9.889 22402 Z= 0.343 Chirality : 0.045 0.279 2754 Planarity : 0.004 0.049 2679 Dihedral : 6.779 57.881 3921 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.57 % Rotamer: Outliers : 3.04 % Allowed : 23.82 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1824 helix: -0.08 (0.27), residues: 391 sheet: 0.07 (0.22), residues: 536 loop : -0.82 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 542 TYR 0.016 0.001 TYR E 217 PHE 0.014 0.001 PHE C 382 TRP 0.018 0.001 TRP C 112 HIS 0.005 0.001 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00588 (16240) covalent geometry : angle 0.67438 (22047) SS BOND : bond 0.00405 ( 38) SS BOND : angle 1.14284 ( 76) hydrogen bonds : bond 0.03676 ( 532) hydrogen bonds : angle 5.08672 ( 1491) link_ALPHA1-2 : bond 0.00558 ( 1) link_ALPHA1-2 : angle 1.59207 ( 3) link_ALPHA1-3 : bond 0.00614 ( 3) link_ALPHA1-3 : angle 1.44830 ( 9) link_ALPHA1-6 : bond 0.01557 ( 1) link_ALPHA1-6 : angle 1.78220 ( 3) link_BETA1-4 : bond 0.00304 ( 31) link_BETA1-4 : angle 1.54465 ( 93) link_NAG-ASN : bond 0.00441 ( 57) link_NAG-ASN : angle 2.49870 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: A 428 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8964 (mp10) REVERT: A 492 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8545 (mp0) REVERT: C 447 SER cc_start: 0.9250 (OUTLIER) cc_final: 0.8748 (m) REVERT: D 530 MET cc_start: 0.8857 (mtp) cc_final: 0.8645 (mtp) REVERT: D 543 ASN cc_start: 0.9111 (t0) cc_final: 0.8854 (t0) REVERT: D 571 TRP cc_start: 0.7936 (m100) cc_final: 0.7598 (m-10) REVERT: E 87 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.9035 (mp0) REVERT: E 102 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8576 (mp0) REVERT: E 426 MET cc_start: 0.9091 (mmm) cc_final: 0.8832 (mmm) REVERT: F 535 MET cc_start: 0.9480 (mtm) cc_final: 0.9225 (mtm) REVERT: F 542 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.7862 (mtm-85) REVERT: F 543 ASN cc_start: 0.9198 (m110) cc_final: 0.8862 (p0) REVERT: F 574 LYS cc_start: 0.9369 (ttpt) cc_final: 0.8980 (ptmt) REVERT: F 584 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8404 (tm-30) REVERT: F 588 ARG cc_start: 0.9235 (ttm170) cc_final: 0.8772 (ttm170) REVERT: H 4 LEU cc_start: 0.8905 (mt) cc_final: 0.8455 (mp) REVERT: L 26 TYR cc_start: 0.8843 (m-80) cc_final: 0.8373 (m-10) REVERT: L 27 MET cc_start: 0.7357 (ttt) cc_final: 0.6868 (tmm) REVERT: L 82 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8234 (mm-30) REVERT: L 84 ASP cc_start: 0.7505 (t0) cc_final: 0.7198 (t0) REVERT: L 94 TYR cc_start: 0.9285 (m-10) cc_final: 0.8954 (m-10) REVERT: L 95 GLU cc_start: 0.8873 (mp0) cc_final: 0.8627 (mp0) outliers start: 50 outliers final: 37 residues processed: 188 average time/residue: 0.1175 time to fit residues: 33.2502 Evaluate side-chains 182 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 117 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 179 optimal weight: 20.0000 chunk 171 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 104 optimal weight: 0.0370 chunk 82 optimal weight: 0.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN D 577 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.052496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039436 restraints weight = 71733.317| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.41 r_work: 0.2671 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16371 Z= 0.118 Angle : 0.650 9.522 22402 Z= 0.314 Chirality : 0.045 0.298 2754 Planarity : 0.004 0.049 2679 Dihedral : 6.415 58.551 3921 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 2.55 % Allowed : 24.24 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.20), residues: 1824 helix: 0.09 (0.28), residues: 378 sheet: 0.13 (0.23), residues: 529 loop : -0.66 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 542 TYR 0.013 0.001 TYR E 217 PHE 0.019 0.001 PHE E 53 TRP 0.019 0.001 TRP F 571 HIS 0.003 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00266 (16240) covalent geometry : angle 0.61757 (22047) SS BOND : bond 0.00231 ( 38) SS BOND : angle 0.85548 ( 76) hydrogen bonds : bond 0.03251 ( 532) hydrogen bonds : angle 4.93858 ( 1491) link_ALPHA1-2 : bond 0.00574 ( 1) link_ALPHA1-2 : angle 1.89296 ( 3) link_ALPHA1-3 : bond 0.00784 ( 3) link_ALPHA1-3 : angle 1.17457 ( 9) link_ALPHA1-6 : bond 0.01835 ( 1) link_ALPHA1-6 : angle 1.49334 ( 3) link_BETA1-4 : bond 0.00449 ( 31) link_BETA1-4 : angle 1.39852 ( 93) link_NAG-ASN : bond 0.00317 ( 57) link_NAG-ASN : angle 2.16123 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3187.98 seconds wall clock time: 55 minutes 47.90 seconds (3347.90 seconds total)