Starting phenix.real_space_refine on Wed Nov 19 03:37:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dfh_7876/11_2025/6dfh_7876.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dfh_7876/11_2025/6dfh_7876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dfh_7876/11_2025/6dfh_7876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dfh_7876/11_2025/6dfh_7876.map" model { file = "/net/cci-nas-00/data/ceres_data/6dfh_7876/11_2025/6dfh_7876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dfh_7876/11_2025/6dfh_7876.cif" } resolution = 3.85 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= 0.000 sd= 0.005 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 120 5.16 5 C 12618 2.51 5 N 3288 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20046 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Chain: "E" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "J" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "D" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: "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: 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: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.01, per 1000 atoms: 0.25 Number of scatterers: 20046 At special positions: 0 Unit cell: (152.44, 156.56, 143.17, 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 120 16.00 O 4020 8.00 N 3288 7.00 C 12618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " 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=2.01 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=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 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=2.01 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 E 605 " distance=2.08 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.01 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=1.99 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 R 4 " - " MAN R 5 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN Z 4 " - " MAN Z 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN h 4 " - " MAN h 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " BMA a 3 " - " MAN a 7 " " BMA i 3 " - " MAN i 7 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 Z 2 " - " BMA Z 3 " " 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 603 " - " ASN A 160 " " NAG A 608 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 626 " - " ASN A 339 " " NAG A 627 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG C 603 " - " ASN C 160 " " NAG C 608 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 626 " - " ASN C 339 " " NAG C 627 " - " ASN C 392 " " NAG D 603 " - " ASN D 160 " " NAG D 608 " - " ASN D 301 " " NAG D 611 " - " ASN D 197 " " NAG D 626 " - " ASN D 339 " " NAG D 627 " - " ASN D 392 " " NAG E 701 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 448 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 276 " " NAG W 1 " - " ASN C 295 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 332 " " NAG b 1 " - " ASN C 448 " " NAG c 1 " - " ASN D 156 " " NAG d 1 " - " ASN D 276 " " NAG e 1 " - " ASN D 295 " " NAG f 1 " - " ASN D 386 " " NAG g 1 " - " ASN D 234 " " NAG h 1 " - " ASN D 262 " " NAG i 1 " - " ASN D 332 " " NAG j 1 " - " ASN D 448 " Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 813.1 milliseconds 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4458 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 54 sheets defined 19.2% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.950A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.603A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 350 removed outlier: 3.543A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.726A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.763A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.595A 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 475 through 484 removed outlier: 3.924A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.592A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.763A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.589A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.714A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.702A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.736A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.628A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.951A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.603A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.543A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.727A pdb=" N PHE C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.762A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.925A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 535 removed outlier: 3.593A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 532 through 535' Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.763A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.589A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 584 " --> pdb=" O VAL E 580 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP E 589 " --> pdb=" O HIS E 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN E 590 " --> pdb=" O TYR E 586 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY E 594 " --> pdb=" O GLN E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 625 Processing helix chain 'E' and resid 628 through 636 removed outlier: 3.714A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 650 removed outlier: 3.702A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 661 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.735A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.628A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.951A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.603A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 350 removed outlier: 3.543A pdb=" N VAL D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.727A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.763A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.925A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 535 removed outlier: 3.593A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 532 through 535' Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.764A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.589A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 628 through 636 removed outlier: 3.714A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 650 removed outlier: 3.702A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 661 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.736A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.628A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.559A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N LYS A 487 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP A 47 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N VAL A 489 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TRP A 45 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ILE A 491 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.620A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU A 260 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU A 260 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 377 removed outlier: 4.332A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.908A pdb=" N ASN A 301 " --> pdb=" O LEU A 323A" (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS A 305 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 67 through 72 Processing sheet with id=AB6, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB8, first strand: chain 'L' and resid 18 through 24 removed outlier: 3.762A pdb=" N CYS L 23 " --> pdb=" O VAL L 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.376A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.558A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 11.229A pdb=" N LYS C 487 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP C 47 " --> pdb=" O LYS C 487 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N VAL C 489 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TRP C 45 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ILE C 491 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.560A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.620A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU C 260 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU C 260 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 374 through 377 removed outlier: 4.331A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 301 through 308 removed outlier: 3.909A pdb=" N ASN C 301 " --> pdb=" O LEU C 323A" (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS C 305 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 67 through 72 Processing sheet with id=AD6, first strand: chain 'G' and resid 98 through 99 Processing sheet with id=AD7, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AD8, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.762A pdb=" N CYS J 23 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.375A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.559A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 11.229A pdb=" N LYS D 487 " --> pdb=" O ASP D 47 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP D 47 " --> pdb=" O LYS D 487 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N VAL D 489 " --> pdb=" O TRP D 45 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TRP D 45 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ILE D 491 " --> pdb=" O PRO D 43 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AE3, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.561A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 173 through 177 Processing sheet with id=AE5, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AE6, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.620A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU D 260 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU D 260 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 374 through 377 removed outlier: 4.331A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 301 through 308 removed outlier: 3.908A pdb=" N ASN D 301 " --> pdb=" O LEU D 323A" (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS D 305 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 67 through 72 Processing sheet with id=AF6, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AF7, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AF8, first strand: chain 'K' and resid 18 through 24 removed outlier: 3.763A pdb=" N CYS K 23 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.375A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1539 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: 4.12 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6187 1.34 - 1.46: 4939 1.46 - 1.58: 9178 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 20466 Sorted by residual: bond pdb=" C5 MAN Z 4 " pdb=" O5 MAN Z 4 " ideal model delta sigma weight residual 1.418 1.466 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C5 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C5 MAN h 4 " pdb=" O5 MAN h 4 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C1 NAG D 608 " pdb=" O5 NAG D 608 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" C5 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.418 1.462 -0.044 2.00e-02 2.50e+03 4.91e+00 ... (remaining 20461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 26450 2.19 - 4.39: 1174 4.39 - 6.58: 123 6.58 - 8.77: 54 8.77 - 10.97: 15 Bond angle restraints: 27816 Sorted by residual: angle pdb=" C GLU A 64 " pdb=" N LYS A 65 " pdb=" CA LYS A 65 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" C GLU D 64 " pdb=" N LYS D 65 " pdb=" CA LYS D 65 " ideal model delta sigma weight residual 121.54 132.49 -10.95 1.91e+00 2.74e-01 3.28e+01 angle pdb=" C GLU C 64 " pdb=" N LYS C 65 " pdb=" CA LYS C 65 " ideal model delta sigma weight residual 121.54 132.42 -10.88 1.91e+00 2.74e-01 3.24e+01 angle pdb=" C GLU C 87 " pdb=" N ASN C 88 " pdb=" CA ASN C 88 " ideal model delta sigma weight residual 122.46 129.15 -6.69 1.41e+00 5.03e-01 2.25e+01 angle pdb=" C GLU D 87 " pdb=" N ASN D 88 " pdb=" CA ASN D 88 " ideal model delta sigma weight residual 122.46 129.15 -6.69 1.41e+00 5.03e-01 2.25e+01 ... (remaining 27811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 12840 22.12 - 44.25: 435 44.25 - 66.37: 57 66.37 - 88.49: 48 88.49 - 110.61: 24 Dihedral angle restraints: 13404 sinusoidal: 6468 harmonic: 6936 Sorted by residual: dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS E 605 " pdb=" CB CYS E 605 " ideal model delta sinusoidal sigma weight residual -86.00 -162.06 76.06 1 1.00e+01 1.00e-02 7.29e+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 -161.94 75.94 1 1.00e+01 1.00e-02 7.27e+01 dihedral pdb=" CB CYS D 501 " pdb=" SG CYS D 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -161.71 75.71 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 13401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2579 0.068 - 0.135: 720 0.135 - 0.203: 78 0.203 - 0.270: 6 0.270 - 0.338: 10 Chirality restraints: 3393 Sorted by residual: chirality pdb=" C5 BMA S 3 " pdb=" C4 BMA S 3 " pdb=" C6 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C5 BMA i 3 " pdb=" C4 BMA i 3 " pdb=" C6 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 3390 not shown) Planarity restraints: 3435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 65 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C LYS D 65 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS D 65 " -0.020 2.00e-02 2.50e+03 pdb=" N HIS D 66 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 65 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.85e+00 pdb=" C LYS A 65 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS A 65 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS A 66 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 65 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C LYS C 65 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS C 65 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS C 66 " 0.017 2.00e-02 2.50e+03 ... (remaining 3432 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4696 2.78 - 3.31: 17698 3.31 - 3.84: 33530 3.84 - 4.37: 36996 4.37 - 4.90: 61133 Nonbonded interactions: 154053 Sorted by model distance: nonbonded pdb=" OE2 GLU D 64 " pdb=" O4 MAN h 4 " model vdw 2.252 3.040 nonbonded pdb=" O THR D 278 " pdb=" O6 NAG d 1 " model vdw 2.257 3.040 nonbonded pdb=" O ASN D 478 " pdb=" OG SER D 481 " model vdw 2.282 3.040 nonbonded pdb=" O ASN C 478 " pdb=" OG SER C 481 " model vdw 2.282 3.040 nonbonded pdb=" O ASN A 478 " pdb=" OG SER A 481 " model vdw 2.283 3.040 ... (remaining 154048 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'Z' selection = chain 'h' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } 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 group one per residue 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: 1.670 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.350 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.009 0.103 20595 Z= 0.413 Angle : 1.097 12.122 28164 Z= 0.537 Chirality : 0.060 0.338 3393 Planarity : 0.007 0.067 3393 Dihedral : 12.651 110.613 8829 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.28 % Allowed : 1.85 % Favored : 97.86 % 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: -4.12 (0.15), residues: 2358 helix: -3.26 (0.18), residues: 354 sheet: -2.19 (0.19), residues: 657 loop : -2.94 (0.14), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 327 TYR 0.024 0.003 TYR C 217 PHE 0.023 0.004 PHE A 391 TRP 0.037 0.004 TRP B 614 HIS 0.008 0.003 HIS D 66 Details of bonding type rmsd covalent geometry : bond 0.00904 (20466) covalent geometry : angle 1.04924 (27816) SS BOND : bond 0.01255 ( 39) SS BOND : angle 1.78222 ( 78) hydrogen bonds : bond 0.27877 ( 564) hydrogen bonds : angle 11.10679 ( 1539) link_ALPHA1-2 : bond 0.00682 ( 9) link_ALPHA1-2 : angle 2.28733 ( 27) link_ALPHA1-3 : bond 0.00333 ( 6) link_ALPHA1-3 : angle 1.98851 ( 18) link_ALPHA1-6 : bond 0.00117 ( 3) link_ALPHA1-6 : angle 2.53479 ( 9) link_BETA1-4 : bond 0.00527 ( 30) link_BETA1-4 : angle 3.11673 ( 90) link_NAG-ASN : bond 0.01383 ( 42) link_NAG-ASN : angle 3.83121 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 274 time to evaluate : 0.850 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.9367 (t) cc_final: 0.8978 (t) REVERT: A 110 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 116 LEU cc_start: 0.9669 (tp) cc_final: 0.9433 (tt) REVERT: A 150 MET cc_start: 0.9446 (mmm) cc_final: 0.8123 (mpp) REVERT: A 195 ASN cc_start: 0.8631 (p0) cc_final: 0.8346 (p0) REVERT: A 328 MET cc_start: 0.8724 (tpt) cc_final: 0.8222 (tpt) REVERT: B 539 VAL cc_start: 0.9350 (t) cc_final: 0.8863 (p) REVERT: B 589 ASP cc_start: 0.9395 (p0) cc_final: 0.8843 (p0) REVERT: B 606 THR cc_start: 0.9436 (p) cc_final: 0.9103 (p) REVERT: B 612 SER cc_start: 0.9162 (p) cc_final: 0.8840 (m) REVERT: B 626 MET cc_start: 0.7987 (mtp) cc_final: 0.7216 (ttm) REVERT: B 648 GLU cc_start: 0.9674 (tt0) cc_final: 0.9132 (pp20) REVERT: B 650 GLN cc_start: 0.6744 (pt0) cc_final: 0.6079 (mp-120) REVERT: L 30 LYS cc_start: 0.9587 (mttt) cc_final: 0.9366 (mtpt) REVERT: C 36 VAL cc_start: 0.9412 (t) cc_final: 0.9119 (t) REVERT: C 150 MET cc_start: 0.9535 (mmm) cc_final: 0.9045 (mmm) REVERT: E 589 ASP cc_start: 0.9425 (p0) cc_final: 0.8685 (p0) REVERT: E 626 MET cc_start: 0.7859 (mtp) cc_final: 0.7318 (ttm) REVERT: E 638 TYR cc_start: 0.8947 (m-80) cc_final: 0.8702 (m-10) REVERT: E 648 GLU cc_start: 0.9617 (tt0) cc_final: 0.9081 (pp20) REVERT: E 654 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8768 (tm-30) REVERT: G 100 GLU cc_start: 0.8415 (tt0) cc_final: 0.8028 (tt0) REVERT: J 30 LYS cc_start: 0.9535 (mttt) cc_final: 0.9320 (mtpt) REVERT: D 36 VAL cc_start: 0.9272 (t) cc_final: 0.8875 (t) REVERT: D 150 MET cc_start: 0.9485 (mmm) cc_final: 0.8000 (mpp) REVERT: D 195 ASN cc_start: 0.8592 (p0) cc_final: 0.8371 (p0) REVERT: D 328 MET cc_start: 0.8851 (tpt) cc_final: 0.8289 (tpt) REVERT: F 589 ASP cc_start: 0.9400 (p0) cc_final: 0.8707 (p0) REVERT: F 612 SER cc_start: 0.9138 (p) cc_final: 0.8832 (m) REVERT: F 626 MET cc_start: 0.7765 (mtp) cc_final: 0.7256 (ttm) REVERT: F 638 TYR cc_start: 0.8984 (m-80) cc_final: 0.8768 (m-10) REVERT: F 648 GLU cc_start: 0.9647 (tt0) cc_final: 0.9167 (pp20) REVERT: F 654 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8817 (tm-30) REVERT: I 100 GLU cc_start: 0.8116 (tt0) cc_final: 0.7904 (tt0) REVERT: K 53 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9098 (mp0) outliers start: 6 outliers final: 0 residues processed: 280 average time/residue: 0.2008 time to fit residues: 79.4629 Evaluate side-chains 154 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 543 ASN C 374 HIS D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.040695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.031625 restraints weight = 147777.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.032686 restraints weight = 80378.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.033421 restraints weight = 54080.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.033913 restraints weight = 41253.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.034242 restraints weight = 34361.609| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20595 Z= 0.221 Angle : 0.790 11.935 28164 Z= 0.395 Chirality : 0.046 0.163 3393 Planarity : 0.005 0.050 3393 Dihedral : 11.322 82.088 4407 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.19 % Allowed : 6.22 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.25 (0.16), residues: 2358 helix: -1.77 (0.22), residues: 423 sheet: -1.77 (0.18), residues: 714 loop : -2.56 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 617 TYR 0.014 0.001 TYR A 217 PHE 0.018 0.002 PHE D 391 TRP 0.018 0.002 TRP E 623 HIS 0.004 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00479 (20466) covalent geometry : angle 0.76010 (27816) SS BOND : bond 0.00658 ( 39) SS BOND : angle 0.94263 ( 78) hydrogen bonds : bond 0.04762 ( 564) hydrogen bonds : angle 7.87382 ( 1539) link_ALPHA1-2 : bond 0.00249 ( 9) link_ALPHA1-2 : angle 1.85453 ( 27) link_ALPHA1-3 : bond 0.00606 ( 6) link_ALPHA1-3 : angle 1.25753 ( 18) link_ALPHA1-6 : bond 0.00396 ( 3) link_ALPHA1-6 : angle 1.42693 ( 9) link_BETA1-4 : bond 0.00340 ( 30) link_BETA1-4 : angle 2.24342 ( 90) link_NAG-ASN : bond 0.00452 ( 42) link_NAG-ASN : angle 2.56799 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.812 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8523 (tm-30) REVERT: A 150 MET cc_start: 0.9460 (mmm) cc_final: 0.9037 (mpp) REVERT: B 530 MET cc_start: 0.7498 (mpp) cc_final: 0.7250 (mpp) REVERT: B 589 ASP cc_start: 0.9096 (p0) cc_final: 0.8716 (p0) REVERT: B 606 THR cc_start: 0.9413 (p) cc_final: 0.9107 (t) REVERT: B 648 GLU cc_start: 0.9572 (tt0) cc_final: 0.9246 (tp30) REVERT: B 650 GLN cc_start: 0.7055 (pt0) cc_final: 0.6047 (mm-40) REVERT: L 30 LYS cc_start: 0.9570 (mttt) cc_final: 0.9319 (mtpt) REVERT: C 110 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 150 MET cc_start: 0.9383 (mmm) cc_final: 0.9109 (tpp) REVERT: E 589 ASP cc_start: 0.9212 (p0) cc_final: 0.8782 (p0) REVERT: E 648 GLU cc_start: 0.9484 (tt0) cc_final: 0.8877 (tp30) REVERT: E 654 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8598 (tm-30) REVERT: G 18 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8302 (mm) REVERT: G 20 LEU cc_start: 0.8928 (mp) cc_final: 0.8268 (tt) REVERT: G 46 GLU cc_start: 0.8802 (tp30) cc_final: 0.8531 (tp30) REVERT: G 100 GLU cc_start: 0.8228 (tt0) cc_final: 0.7840 (tt0) REVERT: J 30 LYS cc_start: 0.9553 (mttt) cc_final: 0.9344 (mtpt) REVERT: D 95 MET cc_start: 0.9002 (tmm) cc_final: 0.8762 (tmm) REVERT: D 150 MET cc_start: 0.9453 (mmm) cc_final: 0.9046 (mmm) REVERT: D 217 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8369 (m-10) REVERT: D 475 MET cc_start: 0.8814 (mmp) cc_final: 0.8582 (mmm) REVERT: F 589 ASP cc_start: 0.9191 (p0) cc_final: 0.8730 (p0) REVERT: F 626 MET cc_start: 0.8345 (mtp) cc_final: 0.8124 (ptp) REVERT: F 648 GLU cc_start: 0.9479 (tt0) cc_final: 0.9028 (tp30) REVERT: F 654 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8639 (tm-30) REVERT: I 20 LEU cc_start: 0.8865 (mp) cc_final: 0.8302 (tt) outliers start: 25 outliers final: 6 residues processed: 203 average time/residue: 0.1623 time to fit residues: 49.9591 Evaluate side-chains 160 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 117 optimal weight: 0.0970 chunk 215 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 39 optimal weight: 0.0970 chunk 194 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 208 optimal weight: 0.5980 chunk 135 optimal weight: 40.0000 chunk 94 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 overall best weight: 2.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 GLN B 652 GLN E 563 GLN E 652 GLN F 563 GLN F 652 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.040570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031473 restraints weight = 147333.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.032556 restraints weight = 78545.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.033308 restraints weight = 52050.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033817 restraints weight = 39407.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.034153 restraints weight = 32603.353| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20595 Z= 0.164 Angle : 0.710 10.900 28164 Z= 0.350 Chirality : 0.045 0.188 3393 Planarity : 0.004 0.041 3393 Dihedral : 9.902 69.715 4407 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.47 % Allowed : 7.64 % Favored : 90.88 % 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: -2.59 (0.17), residues: 2358 helix: -0.84 (0.25), residues: 405 sheet: -1.30 (0.19), residues: 699 loop : -2.30 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 66 TYR 0.018 0.001 TYR B 638 PHE 0.015 0.001 PHE D 391 TRP 0.016 0.002 TRP H 35 HIS 0.003 0.001 HIS I 53 Details of bonding type rmsd covalent geometry : bond 0.00361 (20466) covalent geometry : angle 0.68460 (27816) SS BOND : bond 0.00308 ( 39) SS BOND : angle 1.08535 ( 78) hydrogen bonds : bond 0.03909 ( 564) hydrogen bonds : angle 7.04530 ( 1539) link_ALPHA1-2 : bond 0.00125 ( 9) link_ALPHA1-2 : angle 1.75200 ( 27) link_ALPHA1-3 : bond 0.00729 ( 6) link_ALPHA1-3 : angle 1.17693 ( 18) link_ALPHA1-6 : bond 0.00675 ( 3) link_ALPHA1-6 : angle 1.32996 ( 9) link_BETA1-4 : bond 0.00259 ( 30) link_BETA1-4 : angle 2.00942 ( 90) link_NAG-ASN : bond 0.00308 ( 42) link_NAG-ASN : angle 2.11954 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.768 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 150 MET cc_start: 0.9503 (mmm) cc_final: 0.9048 (mmm) REVERT: B 589 ASP cc_start: 0.9215 (p0) cc_final: 0.8822 (p0) REVERT: B 648 GLU cc_start: 0.9570 (tt0) cc_final: 0.9178 (tp30) REVERT: H 20 LEU cc_start: 0.8952 (mp) cc_final: 0.8333 (tt) REVERT: L 30 LYS cc_start: 0.9561 (mttt) cc_final: 0.9325 (mtpt) REVERT: C 110 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8480 (tm-30) REVERT: C 150 MET cc_start: 0.9456 (mmm) cc_final: 0.9124 (tpp) REVERT: C 475 MET cc_start: 0.8894 (mmp) cc_final: 0.8626 (mmp) REVERT: C 494 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8641 (mm) REVERT: E 530 MET cc_start: 0.7586 (mpp) cc_final: 0.6830 (mpp) REVERT: E 589 ASP cc_start: 0.9229 (p0) cc_final: 0.8859 (p0) REVERT: E 626 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7618 (ptp) REVERT: E 648 GLU cc_start: 0.9511 (tt0) cc_final: 0.8862 (tp30) REVERT: E 654 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8611 (tm-30) REVERT: G 20 LEU cc_start: 0.8916 (mp) cc_final: 0.8297 (tt) REVERT: G 46 GLU cc_start: 0.8864 (tp30) cc_final: 0.8619 (tp30) REVERT: G 100 GLU cc_start: 0.8199 (tt0) cc_final: 0.7727 (tt0) REVERT: G 100 TYR cc_start: 0.8319 (m-10) cc_final: 0.8064 (m-10) REVERT: J 30 LYS cc_start: 0.9543 (mttt) cc_final: 0.9315 (mtpt) REVERT: D 65 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8267 (mmmt) REVERT: D 150 MET cc_start: 0.9427 (mmm) cc_final: 0.9170 (tpp) REVERT: D 217 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8137 (m-10) REVERT: D 475 MET cc_start: 0.8964 (mmp) cc_final: 0.8710 (mmm) REVERT: F 589 ASP cc_start: 0.9172 (p0) cc_final: 0.8765 (p0) REVERT: F 606 THR cc_start: 0.9212 (p) cc_final: 0.8816 (t) REVERT: F 648 GLU cc_start: 0.9525 (tt0) cc_final: 0.9119 (pt0) REVERT: F 650 GLN cc_start: 0.6668 (pt0) cc_final: 0.5996 (mp10) REVERT: I 20 LEU cc_start: 0.8897 (mp) cc_final: 0.8283 (tt) REVERT: I 100 TYR cc_start: 0.8616 (m-10) cc_final: 0.8317 (m-10) outliers start: 31 outliers final: 11 residues processed: 201 average time/residue: 0.1572 time to fit residues: 47.8868 Evaluate side-chains 169 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 92 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 overall best weight: 5.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN H 33 ASN C 82 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN D 82 GLN F 543 ASN ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.039495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.030432 restraints weight = 150545.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.031468 restraints weight = 80368.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.032206 restraints weight = 53718.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032696 restraints weight = 40717.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.033046 restraints weight = 33797.464| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20595 Z= 0.259 Angle : 0.759 10.527 28164 Z= 0.371 Chirality : 0.045 0.195 3393 Planarity : 0.004 0.039 3393 Dihedral : 9.081 63.464 4407 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.52 % Allowed : 9.31 % Favored : 89.17 % 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: -2.38 (0.17), residues: 2358 helix: -0.39 (0.27), residues: 405 sheet: -1.21 (0.19), residues: 720 loop : -2.26 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 500 TYR 0.016 0.002 TYR A 217 PHE 0.015 0.002 PHE D 391 TRP 0.017 0.002 TRP H 35 HIS 0.005 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00562 (20466) covalent geometry : angle 0.73525 (27816) SS BOND : bond 0.00405 ( 39) SS BOND : angle 0.94557 ( 78) hydrogen bonds : bond 0.03688 ( 564) hydrogen bonds : angle 6.76380 ( 1539) link_ALPHA1-2 : bond 0.00430 ( 9) link_ALPHA1-2 : angle 2.00402 ( 27) link_ALPHA1-3 : bond 0.00631 ( 6) link_ALPHA1-3 : angle 1.53503 ( 18) link_ALPHA1-6 : bond 0.00706 ( 3) link_ALPHA1-6 : angle 1.26599 ( 9) link_BETA1-4 : bond 0.00421 ( 30) link_BETA1-4 : angle 1.99677 ( 90) link_NAG-ASN : bond 0.00559 ( 42) link_NAG-ASN : angle 2.17956 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.751 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: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8512 (tm-30) REVERT: B 589 ASP cc_start: 0.9226 (p0) cc_final: 0.8897 (p0) REVERT: B 648 GLU cc_start: 0.9542 (tt0) cc_final: 0.9035 (pt0) REVERT: B 650 GLN cc_start: 0.7067 (pt0) cc_final: 0.6204 (mm-40) REVERT: H 100 TYR cc_start: 0.8834 (m-10) cc_final: 0.8585 (m-80) REVERT: L 30 LYS cc_start: 0.9531 (mttt) cc_final: 0.9293 (mtpt) REVERT: C 110 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8479 (tm-30) REVERT: C 150 MET cc_start: 0.9444 (mmm) cc_final: 0.9144 (tpp) REVERT: C 475 MET cc_start: 0.8998 (mmp) cc_final: 0.8731 (mmp) REVERT: E 589 ASP cc_start: 0.9241 (p0) cc_final: 0.8920 (p0) REVERT: E 626 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7860 (ptp) REVERT: E 648 GLU cc_start: 0.9568 (tt0) cc_final: 0.9056 (tp30) REVERT: E 654 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8605 (tm-30) REVERT: G 20 LEU cc_start: 0.8900 (mp) cc_final: 0.8163 (tt) REVERT: G 46 GLU cc_start: 0.8939 (tp30) cc_final: 0.8703 (tp30) REVERT: G 100 GLU cc_start: 0.8232 (tt0) cc_final: 0.7819 (tt0) REVERT: G 100 TYR cc_start: 0.8531 (m-10) cc_final: 0.7931 (m-10) REVERT: J 30 LYS cc_start: 0.9554 (mttt) cc_final: 0.9324 (mtpt) REVERT: D 95 MET cc_start: 0.9098 (tmm) cc_final: 0.8799 (tmm) REVERT: F 589 ASP cc_start: 0.9193 (p0) cc_final: 0.8952 (p0) REVERT: F 606 THR cc_start: 0.9318 (p) cc_final: 0.8984 (t) REVERT: F 626 MET cc_start: 0.7621 (ptp) cc_final: 0.6964 (ptm) REVERT: F 648 GLU cc_start: 0.9534 (tt0) cc_final: 0.9139 (pt0) REVERT: F 650 GLN cc_start: 0.7212 (pt0) cc_final: 0.6333 (mm-40) REVERT: I 20 LEU cc_start: 0.8964 (mp) cc_final: 0.8290 (tt) REVERT: I 100 TYR cc_start: 0.8573 (m-10) cc_final: 0.8226 (m-10) outliers start: 32 outliers final: 19 residues processed: 194 average time/residue: 0.1660 time to fit residues: 49.1150 Evaluate side-chains 172 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 79 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 60 optimal weight: 0.0970 chunk 3 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN I 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.039532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.030457 restraints weight = 148623.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.031520 restraints weight = 79460.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.032260 restraints weight = 52704.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.032760 restraints weight = 40044.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.033081 restraints weight = 33225.595| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20595 Z= 0.222 Angle : 0.734 15.994 28164 Z= 0.356 Chirality : 0.045 0.202 3393 Planarity : 0.004 0.041 3393 Dihedral : 8.445 60.425 4407 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.71 % Allowed : 10.07 % Favored : 88.22 % 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: -2.24 (0.17), residues: 2358 helix: -0.41 (0.26), residues: 423 sheet: -0.90 (0.19), residues: 675 loop : -2.26 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 66 TYR 0.018 0.001 TYR D 217 PHE 0.014 0.002 PHE D 391 TRP 0.020 0.002 TRP F 623 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00488 (20466) covalent geometry : angle 0.71214 (27816) SS BOND : bond 0.00447 ( 39) SS BOND : angle 0.97664 ( 78) hydrogen bonds : bond 0.03453 ( 564) hydrogen bonds : angle 6.47189 ( 1539) link_ALPHA1-2 : bond 0.00281 ( 9) link_ALPHA1-2 : angle 1.87476 ( 27) link_ALPHA1-3 : bond 0.00792 ( 6) link_ALPHA1-3 : angle 1.50522 ( 18) link_ALPHA1-6 : bond 0.00718 ( 3) link_ALPHA1-6 : angle 1.29195 ( 9) link_BETA1-4 : bond 0.00325 ( 30) link_BETA1-4 : angle 1.84076 ( 90) link_NAG-ASN : bond 0.00463 ( 42) link_NAG-ASN : angle 2.09998 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.827 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: symmetry clash REVERT: A 110 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 166 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7819 (tmm-80) REVERT: A 195 ASN cc_start: 0.7311 (t0) cc_final: 0.6732 (t0) REVERT: B 589 ASP cc_start: 0.9206 (p0) cc_final: 0.8854 (p0) REVERT: B 648 GLU cc_start: 0.9486 (tt0) cc_final: 0.8942 (tp30) REVERT: H 20 LEU cc_start: 0.9089 (mp) cc_final: 0.8458 (tt) REVERT: H 100 GLU cc_start: 0.7942 (tt0) cc_final: 0.7682 (tt0) REVERT: H 100 TYR cc_start: 0.8784 (m-10) cc_final: 0.8515 (m-80) REVERT: H 100 MET cc_start: 0.7322 (ppp) cc_final: 0.7100 (ppp) REVERT: C 150 MET cc_start: 0.9393 (mmm) cc_final: 0.9150 (tpp) REVERT: C 475 MET cc_start: 0.8960 (mmp) cc_final: 0.8712 (mmp) REVERT: E 589 ASP cc_start: 0.9214 (p0) cc_final: 0.8870 (p0) REVERT: E 626 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7833 (ptp) REVERT: E 648 GLU cc_start: 0.9485 (tt0) cc_final: 0.8968 (tp30) REVERT: E 654 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8585 (tm-30) REVERT: G 46 GLU cc_start: 0.8906 (tp30) cc_final: 0.8683 (tp30) REVERT: G 100 TYR cc_start: 0.8472 (m-10) cc_final: 0.7942 (m-10) REVERT: J 30 LYS cc_start: 0.9560 (mttt) cc_final: 0.9332 (mtpt) REVERT: D 65 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8115 (mmmt) REVERT: D 110 GLU cc_start: 0.9203 (tp30) cc_final: 0.8904 (tp30) REVERT: D 475 MET cc_start: 0.8990 (mmp) cc_final: 0.8763 (mmm) REVERT: F 542 ARG cc_start: 0.7977 (tmm-80) cc_final: 0.7485 (tmm-80) REVERT: F 589 ASP cc_start: 0.9152 (p0) cc_final: 0.8788 (p0) REVERT: F 648 GLU cc_start: 0.9501 (tt0) cc_final: 0.9115 (pt0) REVERT: F 650 GLN cc_start: 0.7272 (pt0) cc_final: 0.6379 (mm-40) REVERT: I 100 TYR cc_start: 0.8504 (m-10) cc_final: 0.8127 (m-10) outliers start: 36 outliers final: 16 residues processed: 192 average time/residue: 0.1574 time to fit residues: 46.8455 Evaluate side-chains 171 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 144 optimal weight: 5.9990 chunk 196 optimal weight: 30.0000 chunk 174 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 197 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 58 optimal weight: 0.0270 chunk 35 optimal weight: 0.0020 overall best weight: 1.2648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.040382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.031327 restraints weight = 144742.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.032416 restraints weight = 77332.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.033171 restraints weight = 51169.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033684 restraints weight = 38661.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.034035 restraints weight = 31963.910| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20595 Z= 0.121 Angle : 0.684 14.693 28164 Z= 0.329 Chirality : 0.045 0.196 3393 Planarity : 0.004 0.039 3393 Dihedral : 7.624 56.743 4407 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.19 % Allowed : 10.59 % Favored : 88.22 % 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: -2.06 (0.17), residues: 2358 helix: -0.06 (0.28), residues: 405 sheet: -0.98 (0.19), residues: 720 loop : -2.08 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 542 TYR 0.012 0.001 TYR B 638 PHE 0.012 0.001 PHE D 391 TRP 0.015 0.001 TRP H 35 HIS 0.003 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00267 (20466) covalent geometry : angle 0.66510 (27816) SS BOND : bond 0.00291 ( 39) SS BOND : angle 1.04274 ( 78) hydrogen bonds : bond 0.03151 ( 564) hydrogen bonds : angle 6.23827 ( 1539) link_ALPHA1-2 : bond 0.00131 ( 9) link_ALPHA1-2 : angle 1.68729 ( 27) link_ALPHA1-3 : bond 0.00977 ( 6) link_ALPHA1-3 : angle 1.32339 ( 18) link_ALPHA1-6 : bond 0.00770 ( 3) link_ALPHA1-6 : angle 1.32519 ( 9) link_BETA1-4 : bond 0.00258 ( 30) link_BETA1-4 : angle 1.62391 ( 90) link_NAG-ASN : bond 0.00225 ( 42) link_NAG-ASN : angle 1.85263 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.804 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: symmetry clash REVERT: A 166 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7779 (tmm-80) REVERT: B 589 ASP cc_start: 0.9163 (p0) cc_final: 0.8824 (p0) REVERT: B 626 MET cc_start: 0.7408 (ptp) cc_final: 0.6781 (ptp) REVERT: B 648 GLU cc_start: 0.9442 (tt0) cc_final: 0.8949 (tp30) REVERT: H 20 LEU cc_start: 0.9068 (mp) cc_final: 0.8414 (tt) REVERT: H 100 GLU cc_start: 0.7921 (tt0) cc_final: 0.7704 (tt0) REVERT: H 100 TYR cc_start: 0.8683 (m-10) cc_final: 0.8346 (m-80) REVERT: C 150 MET cc_start: 0.9381 (mmm) cc_final: 0.9103 (tpp) REVERT: C 475 MET cc_start: 0.8941 (mmp) cc_final: 0.8698 (mmp) REVERT: E 589 ASP cc_start: 0.9187 (p0) cc_final: 0.8843 (p0) REVERT: E 648 GLU cc_start: 0.9430 (tt0) cc_final: 0.8905 (tp30) REVERT: E 654 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8575 (tm-30) REVERT: G 46 GLU cc_start: 0.8860 (tp30) cc_final: 0.8644 (tp30) REVERT: G 100 GLU cc_start: 0.8064 (tt0) cc_final: 0.7660 (tt0) REVERT: G 100 TYR cc_start: 0.8411 (m-10) cc_final: 0.8025 (m-10) REVERT: G 100 MET cc_start: 0.7240 (ppp) cc_final: 0.7024 (ppp) REVERT: J 30 LYS cc_start: 0.9500 (mttt) cc_final: 0.9282 (mtpt) REVERT: D 65 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8191 (mmmt) REVERT: D 110 GLU cc_start: 0.9192 (tp30) cc_final: 0.8812 (tp30) REVERT: D 141 MET cc_start: 0.8871 (mmm) cc_final: 0.8646 (mmt) REVERT: D 195 ASN cc_start: 0.7945 (p0) cc_final: 0.7703 (p0) REVERT: D 475 MET cc_start: 0.8944 (mmp) cc_final: 0.8694 (mmm) REVERT: F 542 ARG cc_start: 0.8071 (tmm-80) cc_final: 0.7448 (tmm-80) REVERT: F 589 ASP cc_start: 0.9135 (p0) cc_final: 0.8783 (p0) REVERT: F 606 THR cc_start: 0.9264 (p) cc_final: 0.8936 (t) REVERT: F 626 MET cc_start: 0.7699 (ptm) cc_final: 0.7048 (ptm) REVERT: F 648 GLU cc_start: 0.9460 (tt0) cc_final: 0.8975 (tp30) REVERT: F 650 GLN cc_start: 0.7100 (pt0) cc_final: 0.6300 (mm-40) REVERT: I 81 LYS cc_start: 0.9401 (mtmm) cc_final: 0.9109 (tppt) REVERT: I 100 TYR cc_start: 0.8462 (m-10) cc_final: 0.8249 (m-10) outliers start: 25 outliers final: 12 residues processed: 189 average time/residue: 0.1503 time to fit residues: 43.9591 Evaluate side-chains 169 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 71 optimal weight: 10.0000 chunk 225 optimal weight: 0.0170 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.041021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.031940 restraints weight = 145066.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.033028 restraints weight = 77914.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.033775 restraints weight = 51679.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.034301 restraints weight = 39207.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.034639 restraints weight = 32421.477| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20595 Z= 0.110 Angle : 0.681 13.831 28164 Z= 0.326 Chirality : 0.044 0.210 3393 Planarity : 0.004 0.037 3393 Dihedral : 6.711 51.437 4407 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.04 % Allowed : 11.59 % Favored : 87.37 % 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: -1.90 (0.17), residues: 2358 helix: -0.14 (0.28), residues: 408 sheet: -0.77 (0.20), residues: 690 loop : -1.97 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 542 TYR 0.018 0.001 TYR A 61 PHE 0.010 0.001 PHE D 391 TRP 0.028 0.001 TRP F 623 HIS 0.002 0.000 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00241 (20466) covalent geometry : angle 0.66447 (27816) SS BOND : bond 0.00324 ( 39) SS BOND : angle 0.92315 ( 78) hydrogen bonds : bond 0.03040 ( 564) hydrogen bonds : angle 6.04804 ( 1539) link_ALPHA1-2 : bond 0.00231 ( 9) link_ALPHA1-2 : angle 1.62016 ( 27) link_ALPHA1-3 : bond 0.01040 ( 6) link_ALPHA1-3 : angle 1.42536 ( 18) link_ALPHA1-6 : bond 0.00878 ( 3) link_ALPHA1-6 : angle 1.28552 ( 9) link_BETA1-4 : bond 0.00339 ( 30) link_BETA1-4 : angle 1.50804 ( 90) link_NAG-ASN : bond 0.00196 ( 42) link_NAG-ASN : angle 1.71243 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.709 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.9152 (p0) cc_final: 0.8818 (p0) REVERT: B 626 MET cc_start: 0.7413 (ptp) cc_final: 0.7034 (ptp) REVERT: B 648 GLU cc_start: 0.9433 (tt0) cc_final: 0.9156 (tp30) REVERT: H 100 TYR cc_start: 0.8673 (m-10) cc_final: 0.8319 (m-80) REVERT: C 150 MET cc_start: 0.9356 (mmm) cc_final: 0.9151 (mmm) REVERT: E 530 MET cc_start: 0.8405 (mpp) cc_final: 0.8007 (mmm) REVERT: E 589 ASP cc_start: 0.9166 (p0) cc_final: 0.8822 (p0) REVERT: E 648 GLU cc_start: 0.9446 (tt0) cc_final: 0.8899 (tp30) REVERT: E 654 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8600 (tm-30) REVERT: G 100 GLU cc_start: 0.8089 (tt0) cc_final: 0.7625 (tt0) REVERT: G 100 TYR cc_start: 0.8401 (m-10) cc_final: 0.8072 (m-10) REVERT: G 100 MET cc_start: 0.7123 (ppp) cc_final: 0.6841 (ppp) REVERT: J 30 LYS cc_start: 0.9489 (mttt) cc_final: 0.9250 (mtpt) REVERT: D 65 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8202 (mmmt) REVERT: D 110 GLU cc_start: 0.9219 (tp30) cc_final: 0.8807 (tp30) REVERT: F 589 ASP cc_start: 0.9102 (p0) cc_final: 0.8739 (p0) REVERT: F 626 MET cc_start: 0.7573 (ptm) cc_final: 0.7002 (ptm) REVERT: F 648 GLU cc_start: 0.9438 (tt0) cc_final: 0.8925 (tp30) outliers start: 22 outliers final: 13 residues processed: 187 average time/residue: 0.1443 time to fit residues: 42.1908 Evaluate side-chains 170 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 103 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 165 optimal weight: 0.0570 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 131 optimal weight: 0.0670 overall best weight: 3.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.040033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.030955 restraints weight = 148407.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.032014 restraints weight = 79659.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.032749 restraints weight = 52963.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.033246 restraints weight = 40322.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.033594 restraints weight = 33494.098| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20595 Z= 0.175 Angle : 0.702 12.764 28164 Z= 0.336 Chirality : 0.045 0.231 3393 Planarity : 0.004 0.035 3393 Dihedral : 6.329 45.600 4407 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 1.23 % Allowed : 11.59 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.80 (0.17), residues: 2358 helix: 0.00 (0.28), residues: 408 sheet: -0.63 (0.20), residues: 684 loop : -1.97 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 542 TYR 0.019 0.001 TYR E 586 PHE 0.011 0.001 PHE D 391 TRP 0.018 0.001 TRP F 623 HIS 0.003 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00387 (20466) covalent geometry : angle 0.68434 (27816) SS BOND : bond 0.00311 ( 39) SS BOND : angle 0.90012 ( 78) hydrogen bonds : bond 0.03096 ( 564) hydrogen bonds : angle 6.00981 ( 1539) link_ALPHA1-2 : bond 0.00157 ( 9) link_ALPHA1-2 : angle 1.82247 ( 27) link_ALPHA1-3 : bond 0.00874 ( 6) link_ALPHA1-3 : angle 1.70034 ( 18) link_ALPHA1-6 : bond 0.01018 ( 3) link_ALPHA1-6 : angle 1.03385 ( 9) link_BETA1-4 : bond 0.00298 ( 30) link_BETA1-4 : angle 1.57337 ( 90) link_NAG-ASN : bond 0.00351 ( 42) link_NAG-ASN : angle 1.82347 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.772 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.9184 (p0) cc_final: 0.8879 (p0) REVERT: B 626 MET cc_start: 0.7597 (ptp) cc_final: 0.7190 (ptp) REVERT: B 648 GLU cc_start: 0.9454 (tt0) cc_final: 0.8938 (tp30) REVERT: H 100 TYR cc_start: 0.8743 (m-10) cc_final: 0.8383 (m-80) REVERT: E 589 ASP cc_start: 0.9189 (p0) cc_final: 0.8893 (p0) REVERT: E 648 GLU cc_start: 0.9457 (tt0) cc_final: 0.8932 (tp30) REVERT: E 654 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8594 (tm-30) REVERT: G 20 LEU cc_start: 0.8976 (mp) cc_final: 0.8674 (mt) REVERT: G 100 GLU cc_start: 0.8126 (tt0) cc_final: 0.7634 (tt0) REVERT: G 100 TYR cc_start: 0.8509 (m-10) cc_final: 0.8155 (m-10) REVERT: G 100 MET cc_start: 0.7131 (ppp) cc_final: 0.6822 (ppp) REVERT: D 65 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8213 (mmmt) REVERT: D 110 GLU cc_start: 0.9279 (tp30) cc_final: 0.8840 (tp30) REVERT: F 589 ASP cc_start: 0.9151 (p0) cc_final: 0.8818 (p0) REVERT: F 648 GLU cc_start: 0.9487 (tt0) cc_final: 0.9032 (tp30) outliers start: 26 outliers final: 20 residues processed: 173 average time/residue: 0.1439 time to fit residues: 38.8986 Evaluate side-chains 171 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain I residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 212 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 137 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.040099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.031007 restraints weight = 146231.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.032072 restraints weight = 78385.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.032815 restraints weight = 52158.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.033324 restraints weight = 39556.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033659 restraints weight = 32738.630| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20595 Z= 0.155 Angle : 0.700 12.748 28164 Z= 0.334 Chirality : 0.044 0.219 3393 Planarity : 0.004 0.037 3393 Dihedral : 6.021 43.708 4407 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.23 % Allowed : 11.87 % Favored : 86.89 % 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: -1.75 (0.17), residues: 2358 helix: 0.18 (0.29), residues: 390 sheet: -0.66 (0.20), residues: 699 loop : -1.94 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 151 TYR 0.015 0.001 TYR E 586 PHE 0.011 0.001 PHE D 391 TRP 0.018 0.001 TRP F 623 HIS 0.002 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00344 (20466) covalent geometry : angle 0.68376 (27816) SS BOND : bond 0.00274 ( 39) SS BOND : angle 0.83860 ( 78) hydrogen bonds : bond 0.03031 ( 564) hydrogen bonds : angle 5.90971 ( 1539) link_ALPHA1-2 : bond 0.00065 ( 9) link_ALPHA1-2 : angle 1.73787 ( 27) link_ALPHA1-3 : bond 0.00866 ( 6) link_ALPHA1-3 : angle 1.69996 ( 18) link_ALPHA1-6 : bond 0.01103 ( 3) link_ALPHA1-6 : angle 0.97083 ( 9) link_BETA1-4 : bond 0.00282 ( 30) link_BETA1-4 : angle 1.45388 ( 90) link_NAG-ASN : bond 0.00286 ( 42) link_NAG-ASN : angle 1.79352 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.782 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7805 (tmm-80) REVERT: B 589 ASP cc_start: 0.9159 (p0) cc_final: 0.8846 (p0) REVERT: B 626 MET cc_start: 0.7395 (ptp) cc_final: 0.7029 (ptp) REVERT: B 648 GLU cc_start: 0.9415 (tt0) cc_final: 0.9049 (tp30) REVERT: H 100 TYR cc_start: 0.8709 (m-10) cc_final: 0.8369 (m-80) REVERT: H 100 MET cc_start: 0.7213 (ppp) cc_final: 0.6995 (ppp) REVERT: E 589 ASP cc_start: 0.9197 (p0) cc_final: 0.8906 (p0) REVERT: E 648 GLU cc_start: 0.9433 (tt0) cc_final: 0.8908 (tp30) REVERT: E 654 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8599 (tm-30) REVERT: G 20 LEU cc_start: 0.8988 (mp) cc_final: 0.8670 (mt) REVERT: G 100 GLU cc_start: 0.8016 (tt0) cc_final: 0.7584 (tt0) REVERT: G 100 TYR cc_start: 0.8520 (m-10) cc_final: 0.8173 (m-10) REVERT: G 100 MET cc_start: 0.7117 (ppp) cc_final: 0.6512 (ppp) REVERT: G 107 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.8844 (p) REVERT: D 65 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8191 (mmmt) REVERT: D 110 GLU cc_start: 0.9248 (tp30) cc_final: 0.8809 (tp30) REVERT: D 150 MET cc_start: 0.9454 (mmp) cc_final: 0.8584 (mmt) REVERT: F 589 ASP cc_start: 0.9129 (p0) cc_final: 0.8791 (p0) REVERT: F 648 GLU cc_start: 0.9453 (tt0) cc_final: 0.8992 (tp30) outliers start: 26 outliers final: 17 residues processed: 177 average time/residue: 0.1485 time to fit residues: 40.6571 Evaluate side-chains 169 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 73 optimal weight: 40.0000 chunk 93 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 195 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.029723 restraints weight = 152203.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030749 restraints weight = 81856.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.031452 restraints weight = 54820.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031928 restraints weight = 41911.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032251 restraints weight = 35027.626| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 20595 Z= 0.317 Angle : 0.853 12.686 28164 Z= 0.408 Chirality : 0.047 0.209 3393 Planarity : 0.004 0.033 3393 Dihedral : 6.465 51.323 4407 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 1.09 % Allowed : 12.11 % Favored : 86.80 % 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: -1.87 (0.17), residues: 2358 helix: -0.05 (0.28), residues: 390 sheet: -0.47 (0.20), residues: 687 loop : -2.13 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 327 TYR 0.022 0.002 TYR E 586 PHE 0.013 0.002 PHE C 382 TRP 0.020 0.002 TRP C 395 HIS 0.006 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00691 (20466) covalent geometry : angle 0.83004 (27816) SS BOND : bond 0.00468 ( 39) SS BOND : angle 1.29328 ( 78) hydrogen bonds : bond 0.03543 ( 564) hydrogen bonds : angle 6.09351 ( 1539) link_ALPHA1-2 : bond 0.00566 ( 9) link_ALPHA1-2 : angle 2.26657 ( 27) link_ALPHA1-3 : bond 0.00563 ( 6) link_ALPHA1-3 : angle 2.35967 ( 18) link_ALPHA1-6 : bond 0.01262 ( 3) link_ALPHA1-6 : angle 0.97868 ( 9) link_BETA1-4 : bond 0.00504 ( 30) link_BETA1-4 : angle 1.75800 ( 90) link_NAG-ASN : bond 0.00798 ( 42) link_NAG-ASN : angle 2.31174 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.717 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 150 MET cc_start: 0.9104 (mmt) cc_final: 0.8883 (mmt) REVERT: A 166 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7914 (tmm-80) REVERT: A 201 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9178 (mm) REVERT: B 589 ASP cc_start: 0.9179 (p0) cc_final: 0.8888 (p0) REVERT: B 626 MET cc_start: 0.7524 (ptp) cc_final: 0.7144 (ptp) REVERT: B 648 GLU cc_start: 0.9474 (tt0) cc_final: 0.9082 (tp30) REVERT: H 100 GLU cc_start: 0.7797 (tt0) cc_final: 0.7577 (tt0) REVERT: H 100 TYR cc_start: 0.8834 (m-10) cc_final: 0.8509 (m-80) REVERT: C 475 MET cc_start: 0.9061 (mmm) cc_final: 0.8789 (mmm) REVERT: E 589 ASP cc_start: 0.9229 (p0) cc_final: 0.8963 (p0) REVERT: E 648 GLU cc_start: 0.9496 (tt0) cc_final: 0.8932 (tp30) REVERT: E 654 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8507 (tm-30) REVERT: G 20 LEU cc_start: 0.9150 (mp) cc_final: 0.8833 (mt) REVERT: G 100 GLU cc_start: 0.7970 (tt0) cc_final: 0.7580 (tt0) REVERT: G 100 TYR cc_start: 0.8612 (m-10) cc_final: 0.8038 (m-10) REVERT: G 107 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8852 (p) REVERT: D 65 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8017 (mmmt) REVERT: D 69 TRP cc_start: 0.9497 (OUTLIER) cc_final: 0.9166 (m100) REVERT: D 110 GLU cc_start: 0.9238 (tp30) cc_final: 0.8928 (tp30) REVERT: F 589 ASP cc_start: 0.9197 (p0) cc_final: 0.8906 (p0) REVERT: F 648 GLU cc_start: 0.9477 (tt0) cc_final: 0.9008 (tp30) outliers start: 23 outliers final: 16 residues processed: 157 average time/residue: 0.1449 time to fit residues: 34.8125 Evaluate side-chains 152 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 150 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 213 optimal weight: 0.0870 chunk 53 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.039732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.030612 restraints weight = 148043.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031659 restraints weight = 79165.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.032391 restraints weight = 52912.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.032908 restraints weight = 40147.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.033253 restraints weight = 33288.331| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20595 Z= 0.165 Angle : 0.743 13.014 28164 Z= 0.353 Chirality : 0.045 0.197 3393 Planarity : 0.004 0.037 3393 Dihedral : 6.156 54.391 4407 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.19 % Allowed : 11.92 % Favored : 86.89 % 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: -1.68 (0.17), residues: 2358 helix: 0.36 (0.30), residues: 372 sheet: -0.37 (0.20), residues: 687 loop : -2.06 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.015 0.001 TYR A 217 PHE 0.013 0.001 PHE A 391 TRP 0.016 0.001 TRP F 623 HIS 0.003 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00367 (20466) covalent geometry : angle 0.72608 (27816) SS BOND : bond 0.00267 ( 39) SS BOND : angle 0.95806 ( 78) hydrogen bonds : bond 0.03140 ( 564) hydrogen bonds : angle 5.91051 ( 1539) link_ALPHA1-2 : bond 0.00118 ( 9) link_ALPHA1-2 : angle 1.76757 ( 27) link_ALPHA1-3 : bond 0.00772 ( 6) link_ALPHA1-3 : angle 1.81695 ( 18) link_ALPHA1-6 : bond 0.01157 ( 3) link_ALPHA1-6 : angle 1.14717 ( 9) link_BETA1-4 : bond 0.00282 ( 30) link_BETA1-4 : angle 1.42726 ( 90) link_NAG-ASN : bond 0.00352 ( 42) link_NAG-ASN : angle 1.94103 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.83 seconds wall clock time: 53 minutes 48.26 seconds (3228.26 seconds total)