Starting phenix.real_space_refine on Wed Mar 4 17:24:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0r_20396/03_2026/6v0r_20396.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0r_20396/03_2026/6v0r_20396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v0r_20396/03_2026/6v0r_20396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0r_20396/03_2026/6v0r_20396.map" model { file = "/net/cci-nas-00/data/ceres_data/6v0r_20396/03_2026/6v0r_20396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0r_20396/03_2026/6v0r_20396.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.086 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 108 5.16 5 C 9297 2.51 5 N 2454 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3462 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3462 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "D" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3462 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "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: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.02, per 1000 atoms: 0.20 Number of scatterers: 14910 At special positions: 0 Unit cell: (125.66, 128.75, 119.48, 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 108 16.00 O 3051 8.00 N 2454 7.00 C 9297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.60 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.59 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=2.03 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.60 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS E 561 " distance=2.59 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=2.03 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=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.60 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS F 561 " distance=2.59 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=2.03 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=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 J 4 " - " MAN J 5 " " MAN S 4 " - " MAN S 5 " " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA S 3 " - " MAN S 6 " " BMA b 3 " - " MAN b 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 2 " " NAG V 1 " - " FUC V 3 " " NAG X 1 " - " FUC X 2 " " NAG e 1 " - " FUC e 3 " " NAG g 1 " - " FUC g 2 " NAG-ASN " NAG A 603 " - " ASN A 234 " " NAG A 606 " - " ASN A 392 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 295 " " NAG A 611 " - " ASN A 448 " " NAG A 618 " - " ASN A 301 " " NAG A 622 " - " ASN A 160 " " NAG A 623 " - " ASN A 197 " " NAG A 632 " - " ASN A 355 " " NAG B 703 " - " ASN B 618 " " NAG B 704 " - " ASN B 637 " " NAG C 603 " - " ASN C 234 " " NAG C 606 " - " ASN C 392 " " NAG C 609 " - " ASN C 339 " " NAG C 610 " - " ASN C 295 " " NAG C 611 " - " ASN C 448 " " NAG C 618 " - " ASN C 301 " " NAG C 622 " - " ASN C 160 " " NAG C 623 " - " ASN C 197 " " NAG C 632 " - " ASN C 355 " " NAG D 603 " - " ASN D 234 " " NAG D 606 " - " ASN D 392 " " NAG D 609 " - " ASN D 339 " " NAG D 610 " - " ASN D 295 " " NAG D 611 " - " ASN D 448 " " NAG D 618 " - " ASN D 301 " " NAG D 622 " - " ASN D 160 " " NAG D 623 " - " ASN D 197 " " NAG D 632 " - " ASN D 355 " " NAG E 703 " - " ASN E 618 " " NAG E 704 " - " ASN E 637 " " NAG F 703 " - " ASN F 618 " " NAG F 704 " - " ASN F 637 " " NAG G 1 " - " ASN A 88 " " NAG H 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 386 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 156 " " NAG L 1 " - " ASN A 133 " " NAG M 1 " - " ASN A 137 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN B 611 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 276 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 156 " " NAG U 1 " - " ASN C 133 " " NAG V 1 " - " ASN C 137 " " NAG W 1 " - " ASN C 332 " " NAG X 1 " - " ASN E 611 " " NAG Y 1 " - " ASN D 88 " " NAG Z 1 " - " ASN D 276 " " NAG a 1 " - " ASN D 386 " " NAG b 1 " - " ASN D 262 " " NAG c 1 " - " ASN D 156 " " NAG d 1 " - " ASN D 133 " " NAG e 1 " - " ASN D 137 " " NAG f 1 " - " ASN D 332 " " NAG g 1 " - " ASN F 611 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 455.6 milliseconds 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 27 sheets defined 30.5% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.847A pdb=" N THR A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 3.638A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 5.125A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.935A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.464A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 571 through 596 removed outlier: 4.976A pdb=" N GLN B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.847A pdb=" N THR C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.638A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 5.124A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.935A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.463A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 562 through 568 Processing helix chain 'E' and resid 571 through 596 removed outlier: 4.976A pdb=" N GLN E 577 " --> pdb=" O ILE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 663 Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.847A pdb=" N THR D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 3.638A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 334 through 354 removed outlier: 5.125A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.935A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.463A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 562 through 568 Processing helix chain 'F' and resid 571 through 596 removed outlier: 4.976A pdb=" N GLN F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.373A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.707A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.280A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.732A 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 261 removed outlier: 6.491A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 12.584A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.380A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.373A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.707A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.280A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.491A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 12.584A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.380A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.373A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.707A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.280A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.491A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.451A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP D 457 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ILE D 284 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 271 through 274 removed outlier: 12.584A pdb=" N ILE D 284 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N ASP D 457 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 10.451A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N PHE D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N ILE D 453 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.539A pdb=" N THR D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY D 451 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.380A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2963 1.32 - 1.44: 3799 1.44 - 1.57: 8256 1.57 - 1.70: 24 1.70 - 1.82: 144 Bond restraints: 15186 Sorted by residual: bond pdb=" CB TYR A 484 " pdb=" CG TYR A 484 " ideal model delta sigma weight residual 1.512 1.385 0.127 2.20e-02 2.07e+03 3.32e+01 bond pdb=" CB TYR C 484 " pdb=" CG TYR C 484 " ideal model delta sigma weight residual 1.512 1.385 0.127 2.20e-02 2.07e+03 3.31e+01 bond pdb=" CB TYR D 484 " pdb=" CG TYR D 484 " ideal model delta sigma weight residual 1.512 1.386 0.126 2.20e-02 2.07e+03 3.29e+01 bond pdb=" CB TYR C 217 " pdb=" CG TYR C 217 " ideal model delta sigma weight residual 1.512 1.410 0.102 2.20e-02 2.07e+03 2.16e+01 bond pdb=" CB TYR A 217 " pdb=" CG TYR A 217 " ideal model delta sigma weight residual 1.512 1.410 0.102 2.20e-02 2.07e+03 2.15e+01 ... (remaining 15181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 19894 4.29 - 8.57: 704 8.57 - 12.86: 15 12.86 - 17.15: 0 17.15 - 21.44: 3 Bond angle restraints: 20616 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.01e+00 9.80e-01 6.19e+01 angle pdb=" C ARG D 298 " pdb=" N PRO D 299 " pdb=" CA PRO D 299 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.01e+00 9.80e-01 6.15e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.01e+00 9.80e-01 6.15e+01 angle pdb=" C4 FUC X 2 " pdb=" C5 FUC X 2 " pdb=" C6 FUC X 2 " ideal model delta sigma weight residual 113.23 91.79 21.44 3.00e+00 1.11e-01 5.11e+01 angle pdb=" C4 FUC O 2 " pdb=" C5 FUC O 2 " pdb=" C6 FUC O 2 " ideal model delta sigma weight residual 113.23 91.80 21.43 3.00e+00 1.11e-01 5.10e+01 ... (remaining 20611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 9945 21.81 - 43.62: 389 43.62 - 65.42: 112 65.42 - 87.23: 57 87.23 - 109.04: 36 Dihedral angle restraints: 10539 sinusoidal: 5619 harmonic: 4920 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.54 -60.54 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.53 -60.53 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 153.53 -60.53 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 10536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1960 0.114 - 0.229: 595 0.229 - 0.343: 82 0.343 - 0.457: 0 0.457 - 0.571: 12 Chirality restraints: 2649 Sorted by residual: chirality pdb=" C1 FUC X 2 " pdb=" O6 NAG X 1 " pdb=" C2 FUC X 2 " pdb=" O5 FUC X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.38e+02 chirality pdb=" C1 FUC g 2 " pdb=" O6 NAG g 1 " pdb=" C2 FUC g 2 " pdb=" O5 FUC g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 FUC O 2 " pdb=" O6 NAG O 1 " pdb=" C2 FUC O 2 " pdb=" O5 FUC O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.34e+02 ... (remaining 2646 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.052 2.00e-02 2.50e+03 5.46e-02 3.72e+01 pdb=" CG ASN F 611 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.052 2.00e-02 2.50e+03 5.46e-02 3.72e+01 pdb=" CG ASN B 611 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " -0.052 2.00e-02 2.50e+03 5.46e-02 3.72e+01 pdb=" CG ASN E 611 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " -0.065 2.00e-02 2.50e+03 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3970 2.80 - 3.32: 13044 3.32 - 3.85: 24377 3.85 - 4.37: 28026 4.37 - 4.90: 46220 Nonbonded interactions: 115637 Sorted by model distance: nonbonded pdb=" OG1 THR D 37 " pdb=" OG1 THR D 499 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.270 3.040 nonbonded pdb=" O5 NAG H 1 " pdb=" O6 NAG H 1 " model vdw 2.383 2.432 nonbonded pdb=" O5 NAG Z 1 " pdb=" O6 NAG Z 1 " model vdw 2.383 2.432 ... (remaining 115632 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: 0.02 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' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'b' } ncs_group { reference = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.960 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.023 0.570 15330 Z= 1.191 Angle : 1.880 21.716 21012 Z= 1.128 Chirality : 0.106 0.571 2649 Planarity : 0.009 0.049 2469 Dihedral : 14.988 109.037 7239 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 1.44 % Allowed : 4.32 % Favored : 94.24 % Rotamer: Outliers : 1.98 % Allowed : 1.19 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1668 helix: -0.30 (0.25), residues: 402 sheet: 0.77 (0.23), residues: 501 loop : 0.88 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 298 TYR 0.048 0.008 TYR C 40 PHE 0.038 0.006 PHE A 383 TRP 0.037 0.011 TRP A 479 HIS 0.006 0.002 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.01982 (15186) covalent geometry : angle 1.79986 (20616) SS BOND : bond 0.23056 ( 36) SS BOND : angle 7.90907 ( 72) hydrogen bonds : bond 0.18370 ( 573) hydrogen bonds : angle 7.15498 ( 1557) link_ALPHA1-2 : bond 0.03745 ( 3) link_ALPHA1-2 : angle 2.67659 ( 9) link_ALPHA1-3 : bond 0.03424 ( 3) link_ALPHA1-3 : angle 2.51662 ( 9) link_ALPHA1-6 : bond 0.03692 ( 3) link_ALPHA1-6 : angle 3.19547 ( 9) link_BETA1-4 : bond 0.02831 ( 33) link_BETA1-4 : angle 3.80013 ( 99) link_BETA1-6 : bond 0.01700 ( 6) link_BETA1-6 : angle 4.66855 ( 18) link_NAG-ASN : bond 0.03061 ( 60) link_NAG-ASN : angle 2.32995 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 378 time to evaluate : 0.505 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 95 MET cc_start: 0.8353 (ptm) cc_final: 0.8145 (ptp) REVERT: A 103 GLN cc_start: 0.8742 (tp40) cc_final: 0.8463 (tm-30) REVERT: A 199 SER cc_start: 0.9331 (p) cc_final: 0.9098 (m) REVERT: A 457 ASP cc_start: 0.7819 (t0) cc_final: 0.7562 (t0) REVERT: B 530 MET cc_start: 0.8076 (mtp) cc_final: 0.7746 (mtp) REVERT: B 543 ASN cc_start: 0.8864 (m-40) cc_final: 0.8448 (m-40) REVERT: B 612 SER cc_start: 0.8439 (p) cc_final: 0.8161 (t) REVERT: B 647 GLU cc_start: 0.7662 (tt0) cc_final: 0.7432 (mt-10) REVERT: C 103 GLN cc_start: 0.8770 (tp40) cc_final: 0.8368 (tm-30) REVERT: C 107 ASP cc_start: 0.7888 (m-30) cc_final: 0.7674 (m-30) REVERT: C 109 ILE cc_start: 0.9178 (mt) cc_final: 0.8946 (tt) REVERT: C 199 SER cc_start: 0.9283 (p) cc_final: 0.9002 (m) REVERT: C 457 ASP cc_start: 0.7906 (t0) cc_final: 0.7705 (t0) REVERT: E 530 MET cc_start: 0.8137 (mtp) cc_final: 0.7702 (mtp) REVERT: E 543 ASN cc_start: 0.8873 (m-40) cc_final: 0.8530 (m-40) REVERT: E 612 SER cc_start: 0.8532 (p) cc_final: 0.8268 (t) REVERT: E 623 TRP cc_start: 0.8897 (m100) cc_final: 0.8510 (m100) REVERT: E 628 TRP cc_start: 0.8862 (m100) cc_final: 0.8651 (m100) REVERT: D 103 GLN cc_start: 0.8771 (tp40) cc_final: 0.8464 (tm-30) REVERT: D 127 VAL cc_start: 0.9048 (m) cc_final: 0.8840 (p) REVERT: D 199 SER cc_start: 0.9291 (p) cc_final: 0.8980 (m) REVERT: D 457 ASP cc_start: 0.8032 (t0) cc_final: 0.7799 (t0) REVERT: D 486 TYR cc_start: 0.9108 (m-80) cc_final: 0.8893 (m-80) REVERT: F 530 MET cc_start: 0.8093 (mtp) cc_final: 0.7460 (mtp) REVERT: F 543 ASN cc_start: 0.8787 (m-40) cc_final: 0.8309 (m-40) REVERT: F 562 GLN cc_start: 0.6936 (mp10) cc_final: 0.6663 (mt0) REVERT: F 612 SER cc_start: 0.8402 (p) cc_final: 0.8065 (t) REVERT: F 615 SER cc_start: 0.9282 (t) cc_final: 0.9001 (t) REVERT: F 628 TRP cc_start: 0.8904 (m100) cc_final: 0.8670 (m100) outliers start: 30 outliers final: 12 residues processed: 399 average time/residue: 0.1141 time to fit residues: 66.7688 Evaluate side-chains 200 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain F residue 544 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 478 ASN B 575 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 478 ASN E 575 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN D 478 ASN F 575 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106692 restraints weight = 22356.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108136 restraints weight = 17934.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108983 restraints weight = 15330.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109870 restraints weight = 13722.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110057 restraints weight = 12601.944| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15330 Z= 0.194 Angle : 0.872 9.250 21012 Z= 0.430 Chirality : 0.047 0.185 2649 Planarity : 0.004 0.028 2469 Dihedral : 12.001 82.284 4034 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.86 % Favored : 94.78 % Rotamer: Outliers : 2.64 % Allowed : 9.75 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1668 helix: 1.21 (0.28), residues: 369 sheet: 0.44 (0.23), residues: 507 loop : 0.51 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.016 0.002 TYR D 173 PHE 0.025 0.002 PHE C 53 TRP 0.015 0.002 TRP D 479 HIS 0.006 0.001 HIS E 564 Details of bonding type rmsd covalent geometry : bond 0.00434 (15186) covalent geometry : angle 0.81464 (20616) SS BOND : bond 0.00561 ( 36) SS BOND : angle 1.86819 ( 72) hydrogen bonds : bond 0.07235 ( 573) hydrogen bonds : angle 5.68680 ( 1557) link_ALPHA1-2 : bond 0.00743 ( 3) link_ALPHA1-2 : angle 1.48743 ( 9) link_ALPHA1-3 : bond 0.01171 ( 3) link_ALPHA1-3 : angle 1.80758 ( 9) link_ALPHA1-6 : bond 0.00586 ( 3) link_ALPHA1-6 : angle 1.98709 ( 9) link_BETA1-4 : bond 0.00572 ( 33) link_BETA1-4 : angle 2.70275 ( 99) link_BETA1-6 : bond 0.00424 ( 6) link_BETA1-6 : angle 1.22932 ( 18) link_NAG-ASN : bond 0.00357 ( 60) link_NAG-ASN : angle 2.60125 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8543 (tp40) cc_final: 0.8287 (tm-30) REVERT: A 199 SER cc_start: 0.9298 (p) cc_final: 0.9056 (m) REVERT: B 530 MET cc_start: 0.8125 (mtp) cc_final: 0.7702 (mtp) REVERT: B 535 MET cc_start: 0.8650 (mmt) cc_final: 0.8341 (mpp) REVERT: B 543 ASN cc_start: 0.8589 (m-40) cc_final: 0.8232 (m-40) REVERT: B 612 SER cc_start: 0.7691 (p) cc_final: 0.7310 (t) REVERT: B 616 ASN cc_start: 0.8048 (t0) cc_final: 0.7351 (p0) REVERT: C 107 ASP cc_start: 0.7606 (m-30) cc_final: 0.7131 (m-30) REVERT: C 199 SER cc_start: 0.9271 (p) cc_final: 0.8982 (m) REVERT: C 452 LEU cc_start: 0.9123 (mt) cc_final: 0.8908 (mp) REVERT: E 612 SER cc_start: 0.8135 (p) cc_final: 0.7798 (t) REVERT: E 616 ASN cc_start: 0.7919 (t0) cc_final: 0.7265 (p0) REVERT: D 199 SER cc_start: 0.9368 (p) cc_final: 0.8988 (m) REVERT: D 502 LYS cc_start: 0.8336 (tttm) cc_final: 0.8091 (tttt) REVERT: F 530 MET cc_start: 0.7821 (mtp) cc_final: 0.7333 (mtp) REVERT: F 612 SER cc_start: 0.7930 (p) cc_final: 0.7623 (m) REVERT: F 616 ASN cc_start: 0.7847 (t0) cc_final: 0.7040 (p0) outliers start: 40 outliers final: 28 residues processed: 254 average time/residue: 0.1051 time to fit residues: 40.2867 Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 130 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.083341 restraints weight = 24228.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.085181 restraints weight = 18238.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.086498 restraints weight = 14940.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.087280 restraints weight = 12977.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.087923 restraints weight = 11794.346| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15330 Z= 0.196 Angle : 0.768 9.097 21012 Z= 0.379 Chirality : 0.046 0.215 2649 Planarity : 0.004 0.039 2469 Dihedral : 8.952 72.112 4026 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.22 % Favored : 94.42 % Rotamer: Outliers : 3.29 % Allowed : 10.74 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1668 helix: 0.74 (0.27), residues: 405 sheet: 0.01 (0.24), residues: 417 loop : 0.43 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 617 TYR 0.018 0.002 TYR A 484 PHE 0.017 0.002 PHE D 176 TRP 0.019 0.002 TRP F 623 HIS 0.010 0.002 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00450 (15186) covalent geometry : angle 0.72643 (20616) SS BOND : bond 0.00757 ( 36) SS BOND : angle 1.60539 ( 72) hydrogen bonds : bond 0.05610 ( 573) hydrogen bonds : angle 5.19694 ( 1557) link_ALPHA1-2 : bond 0.00557 ( 3) link_ALPHA1-2 : angle 2.20071 ( 9) link_ALPHA1-3 : bond 0.01172 ( 3) link_ALPHA1-3 : angle 1.26192 ( 9) link_ALPHA1-6 : bond 0.00779 ( 3) link_ALPHA1-6 : angle 1.98149 ( 9) link_BETA1-4 : bond 0.00496 ( 33) link_BETA1-4 : angle 1.96144 ( 99) link_BETA1-6 : bond 0.00243 ( 6) link_BETA1-6 : angle 1.25665 ( 18) link_NAG-ASN : bond 0.00385 ( 60) link_NAG-ASN : angle 2.12925 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.516 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 199 SER cc_start: 0.9361 (p) cc_final: 0.8980 (m) REVERT: B 612 SER cc_start: 0.8244 (p) cc_final: 0.7976 (t) REVERT: B 616 ASN cc_start: 0.8125 (t0) cc_final: 0.7553 (p0) REVERT: C 199 SER cc_start: 0.9381 (p) cc_final: 0.8898 (m) REVERT: E 616 ASN cc_start: 0.8046 (t0) cc_final: 0.7358 (p0) REVERT: D 100 MET cc_start: 0.8830 (mtp) cc_final: 0.8590 (mtm) REVERT: D 199 SER cc_start: 0.9435 (p) cc_final: 0.8972 (m) REVERT: D 207 LYS cc_start: 0.8536 (tppt) cc_final: 0.8238 (mmtm) REVERT: F 616 ASN cc_start: 0.7905 (t0) cc_final: 0.7263 (p0) REVERT: F 617 ARG cc_start: 0.8652 (mtt90) cc_final: 0.8438 (mtp180) outliers start: 50 outliers final: 39 residues processed: 236 average time/residue: 0.1026 time to fit residues: 36.4582 Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 0.0870 chunk 155 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS B 577 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS F 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103649 restraints weight = 23801.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106812 restraints weight = 15319.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108893 restraints weight = 11435.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110281 restraints weight = 9406.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111157 restraints weight = 8212.163| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 15330 Z= 0.284 Angle : 0.807 8.077 21012 Z= 0.396 Chirality : 0.048 0.229 2649 Planarity : 0.005 0.048 2469 Dihedral : 8.318 65.214 4023 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.28 % Favored : 94.36 % Rotamer: Outliers : 4.48 % Allowed : 11.73 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1668 helix: 0.95 (0.28), residues: 405 sheet: -0.27 (0.24), residues: 417 loop : -0.01 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 166 TYR 0.014 0.002 TYR A 484 PHE 0.026 0.003 PHE C 53 TRP 0.017 0.002 TRP F 623 HIS 0.004 0.001 HIS E 564 Details of bonding type rmsd covalent geometry : bond 0.00675 (15186) covalent geometry : angle 0.76938 (20616) SS BOND : bond 0.00709 ( 36) SS BOND : angle 1.52047 ( 72) hydrogen bonds : bond 0.05822 ( 573) hydrogen bonds : angle 5.18597 ( 1557) link_ALPHA1-2 : bond 0.00364 ( 3) link_ALPHA1-2 : angle 2.13460 ( 9) link_ALPHA1-3 : bond 0.01058 ( 3) link_ALPHA1-3 : angle 1.53826 ( 9) link_ALPHA1-6 : bond 0.00709 ( 3) link_ALPHA1-6 : angle 1.90908 ( 9) link_BETA1-4 : bond 0.00423 ( 33) link_BETA1-4 : angle 1.79237 ( 99) link_BETA1-6 : bond 0.00324 ( 6) link_BETA1-6 : angle 1.07781 ( 18) link_NAG-ASN : bond 0.00433 ( 60) link_NAG-ASN : angle 2.21282 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7876 (ttp80) REVERT: A 199 SER cc_start: 0.9528 (p) cc_final: 0.9084 (m) REVERT: B 612 SER cc_start: 0.8723 (p) cc_final: 0.8491 (t) REVERT: B 616 ASN cc_start: 0.8501 (t0) cc_final: 0.7791 (p0) REVERT: C 125 LEU cc_start: 0.9250 (tp) cc_final: 0.8768 (tp) REVERT: C 199 SER cc_start: 0.9529 (p) cc_final: 0.9207 (m) REVERT: C 207 LYS cc_start: 0.8735 (tppt) cc_final: 0.7921 (tmtt) REVERT: E 612 SER cc_start: 0.8672 (m) cc_final: 0.8254 (t) REVERT: E 616 ASN cc_start: 0.8533 (t0) cc_final: 0.7797 (p0) REVERT: D 125 LEU cc_start: 0.9158 (tp) cc_final: 0.8490 (tp) REVERT: D 199 SER cc_start: 0.9522 (p) cc_final: 0.8911 (m) REVERT: D 207 LYS cc_start: 0.8773 (tppt) cc_final: 0.8424 (mttm) REVERT: F 616 ASN cc_start: 0.8423 (t0) cc_final: 0.7561 (p0) outliers start: 68 outliers final: 46 residues processed: 224 average time/residue: 0.1045 time to fit residues: 35.7984 Evaluate side-chains 207 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 663 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.130243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108048 restraints weight = 23708.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111368 restraints weight = 14897.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113603 restraints weight = 10969.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114984 restraints weight = 8896.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115997 restraints weight = 7735.692| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15330 Z= 0.138 Angle : 0.668 7.434 21012 Z= 0.325 Chirality : 0.044 0.262 2649 Planarity : 0.003 0.038 2469 Dihedral : 7.629 58.382 4023 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.68 % Favored : 94.96 % Rotamer: Outliers : 2.83 % Allowed : 14.16 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1668 helix: 0.81 (0.27), residues: 429 sheet: -0.21 (0.25), residues: 417 loop : -0.02 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 617 TYR 0.012 0.001 TYR A 217 PHE 0.024 0.002 PHE C 53 TRP 0.015 0.001 TRP F 623 HIS 0.004 0.001 HIS E 564 Details of bonding type rmsd covalent geometry : bond 0.00314 (15186) covalent geometry : angle 0.62991 (20616) SS BOND : bond 0.00430 ( 36) SS BOND : angle 1.16404 ( 72) hydrogen bonds : bond 0.04804 ( 573) hydrogen bonds : angle 4.86342 ( 1557) link_ALPHA1-2 : bond 0.00412 ( 3) link_ALPHA1-2 : angle 2.15007 ( 9) link_ALPHA1-3 : bond 0.01260 ( 3) link_ALPHA1-3 : angle 1.18601 ( 9) link_ALPHA1-6 : bond 0.00767 ( 3) link_ALPHA1-6 : angle 1.84069 ( 9) link_BETA1-4 : bond 0.00443 ( 33) link_BETA1-4 : angle 1.53251 ( 99) link_BETA1-6 : bond 0.00320 ( 6) link_BETA1-6 : angle 1.14741 ( 18) link_NAG-ASN : bond 0.00309 ( 60) link_NAG-ASN : angle 2.06612 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9537 (p) cc_final: 0.9065 (m) REVERT: A 207 LYS cc_start: 0.8687 (tppt) cc_final: 0.8350 (mttp) REVERT: B 612 SER cc_start: 0.8677 (p) cc_final: 0.8412 (t) REVERT: B 616 ASN cc_start: 0.8459 (t0) cc_final: 0.7794 (p0) REVERT: C 125 LEU cc_start: 0.9220 (tp) cc_final: 0.8772 (tp) REVERT: C 199 SER cc_start: 0.9515 (p) cc_final: 0.9190 (m) REVERT: C 207 LYS cc_start: 0.8601 (tppt) cc_final: 0.7829 (tmtt) REVERT: E 612 SER cc_start: 0.8619 (m) cc_final: 0.8204 (t) REVERT: E 616 ASN cc_start: 0.8518 (t0) cc_final: 0.7768 (p0) REVERT: E 647 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6946 (mt-10) REVERT: E 653 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: D 125 LEU cc_start: 0.9110 (tp) cc_final: 0.8429 (tp) REVERT: D 199 SER cc_start: 0.9487 (p) cc_final: 0.9051 (m) REVERT: D 207 LYS cc_start: 0.8590 (tppt) cc_final: 0.8330 (mmtm) REVERT: D 209 SER cc_start: 0.8793 (t) cc_final: 0.8270 (p) REVERT: D 340 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7553 (tm-30) REVERT: F 616 ASN cc_start: 0.8277 (t0) cc_final: 0.7580 (p0) outliers start: 43 outliers final: 34 residues processed: 221 average time/residue: 0.1122 time to fit residues: 37.1232 Evaluate side-chains 201 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 663 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 118 optimal weight: 0.0060 chunk 11 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.130180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108078 restraints weight = 23356.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111339 restraints weight = 14788.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113483 restraints weight = 10926.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114912 restraints weight = 8927.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115875 restraints weight = 7748.018| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15330 Z= 0.143 Angle : 0.652 6.913 21012 Z= 0.315 Chirality : 0.044 0.236 2649 Planarity : 0.004 0.039 2469 Dihedral : 7.154 51.306 4023 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.10 % Favored : 94.54 % Rotamer: Outliers : 3.56 % Allowed : 14.36 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1668 helix: 0.85 (0.27), residues: 429 sheet: -0.21 (0.25), residues: 417 loop : -0.10 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 166 TYR 0.012 0.001 TYR D 486 PHE 0.011 0.002 PHE D 383 TRP 0.012 0.001 TRP F 623 HIS 0.003 0.001 HIS E 564 Details of bonding type rmsd covalent geometry : bond 0.00330 (15186) covalent geometry : angle 0.61580 (20616) SS BOND : bond 0.00388 ( 36) SS BOND : angle 1.05110 ( 72) hydrogen bonds : bond 0.04555 ( 573) hydrogen bonds : angle 4.71419 ( 1557) link_ALPHA1-2 : bond 0.00398 ( 3) link_ALPHA1-2 : angle 2.06478 ( 9) link_ALPHA1-3 : bond 0.01254 ( 3) link_ALPHA1-3 : angle 1.08321 ( 9) link_ALPHA1-6 : bond 0.00687 ( 3) link_ALPHA1-6 : angle 1.65991 ( 9) link_BETA1-4 : bond 0.00458 ( 33) link_BETA1-4 : angle 1.56434 ( 99) link_BETA1-6 : bond 0.00354 ( 6) link_BETA1-6 : angle 1.12719 ( 18) link_NAG-ASN : bond 0.00317 ( 60) link_NAG-ASN : angle 1.95299 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8451 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 166 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7914 (ttp80) REVERT: A 199 SER cc_start: 0.9535 (p) cc_final: 0.9070 (m) REVERT: A 207 LYS cc_start: 0.8614 (tppt) cc_final: 0.8293 (mttp) REVERT: A 209 SER cc_start: 0.8803 (t) cc_final: 0.8332 (p) REVERT: A 486 TYR cc_start: 0.8929 (m-80) cc_final: 0.8510 (m-10) REVERT: B 612 SER cc_start: 0.8693 (p) cc_final: 0.8462 (t) REVERT: B 616 ASN cc_start: 0.8473 (t0) cc_final: 0.7810 (p0) REVERT: B 620 SER cc_start: 0.8716 (m) cc_final: 0.8463 (t) REVERT: C 199 SER cc_start: 0.9531 (p) cc_final: 0.9228 (m) REVERT: C 207 LYS cc_start: 0.8554 (tppt) cc_final: 0.8288 (mmtm) REVERT: C 209 SER cc_start: 0.8942 (t) cc_final: 0.8436 (p) REVERT: E 612 SER cc_start: 0.8719 (m) cc_final: 0.8290 (t) REVERT: E 616 ASN cc_start: 0.8526 (t0) cc_final: 0.7825 (p0) REVERT: E 653 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8547 (tm-30) REVERT: D 125 LEU cc_start: 0.9103 (tp) cc_final: 0.8404 (tp) REVERT: D 199 SER cc_start: 0.9517 (p) cc_final: 0.9151 (m) REVERT: D 207 LYS cc_start: 0.8597 (tppt) cc_final: 0.8396 (mmtm) REVERT: D 209 SER cc_start: 0.8879 (t) cc_final: 0.8354 (p) REVERT: D 340 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7529 (tm-30) REVERT: F 616 ASN cc_start: 0.8339 (t0) cc_final: 0.7655 (p0) outliers start: 54 outliers final: 41 residues processed: 224 average time/residue: 0.1074 time to fit residues: 36.5013 Evaluate side-chains 215 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 0.0770 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111860 restraints weight = 24345.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115076 restraints weight = 15407.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117344 restraints weight = 11469.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118793 restraints weight = 9323.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119832 restraints weight = 8102.613| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15330 Z= 0.171 Angle : 0.667 6.462 21012 Z= 0.323 Chirality : 0.044 0.243 2649 Planarity : 0.004 0.041 2469 Dihedral : 6.975 54.396 4021 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.64 % Favored : 94.00 % Rotamer: Outliers : 3.62 % Allowed : 14.56 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1668 helix: 0.95 (0.27), residues: 429 sheet: -0.20 (0.25), residues: 417 loop : -0.22 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 542 TYR 0.019 0.001 TYR D 217 PHE 0.024 0.002 PHE C 53 TRP 0.010 0.001 TRP D 96 HIS 0.003 0.001 HIS E 564 Details of bonding type rmsd covalent geometry : bond 0.00403 (15186) covalent geometry : angle 0.63296 (20616) SS BOND : bond 0.00434 ( 36) SS BOND : angle 1.03556 ( 72) hydrogen bonds : bond 0.04646 ( 573) hydrogen bonds : angle 4.70353 ( 1557) link_ALPHA1-2 : bond 0.00369 ( 3) link_ALPHA1-2 : angle 2.07614 ( 9) link_ALPHA1-3 : bond 0.01237 ( 3) link_ALPHA1-3 : angle 1.03298 ( 9) link_ALPHA1-6 : bond 0.00476 ( 3) link_ALPHA1-6 : angle 1.55948 ( 9) link_BETA1-4 : bond 0.00452 ( 33) link_BETA1-4 : angle 1.61515 ( 99) link_BETA1-6 : bond 0.00318 ( 6) link_BETA1-6 : angle 1.11701 ( 18) link_NAG-ASN : bond 0.00321 ( 60) link_NAG-ASN : angle 1.92305 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.510 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 166 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7729 (ttp80) REVERT: A 199 SER cc_start: 0.9546 (p) cc_final: 0.9099 (m) REVERT: A 207 LYS cc_start: 0.8600 (tppt) cc_final: 0.8108 (tmtt) REVERT: A 209 SER cc_start: 0.8813 (t) cc_final: 0.8456 (p) REVERT: B 616 ASN cc_start: 0.8494 (t0) cc_final: 0.7902 (p0) REVERT: B 620 SER cc_start: 0.8724 (m) cc_final: 0.8445 (t) REVERT: C 125 LEU cc_start: 0.9220 (tp) cc_final: 0.8773 (tp) REVERT: C 199 SER cc_start: 0.9536 (p) cc_final: 0.9225 (m) REVERT: C 207 LYS cc_start: 0.8495 (tppt) cc_final: 0.8254 (mmtm) REVERT: C 209 SER cc_start: 0.8956 (t) cc_final: 0.8456 (p) REVERT: E 612 SER cc_start: 0.8871 (m) cc_final: 0.8518 (t) REVERT: E 616 ASN cc_start: 0.8577 (t0) cc_final: 0.8343 (t0) REVERT: D 107 ASP cc_start: 0.8497 (m-30) cc_final: 0.8148 (t0) REVERT: D 125 LEU cc_start: 0.9206 (tp) cc_final: 0.8547 (tp) REVERT: D 199 SER cc_start: 0.9550 (p) cc_final: 0.9183 (m) REVERT: D 207 LYS cc_start: 0.8531 (tppt) cc_final: 0.8302 (mmtm) REVERT: D 209 SER cc_start: 0.8871 (t) cc_final: 0.8445 (p) REVERT: D 340 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7558 (tm-30) REVERT: F 616 ASN cc_start: 0.8357 (t0) cc_final: 0.7663 (p0) outliers start: 55 outliers final: 46 residues processed: 229 average time/residue: 0.1023 time to fit residues: 35.8589 Evaluate side-chains 221 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 150 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 0.0270 overall best weight: 0.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.130139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107894 restraints weight = 23766.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111108 restraints weight = 15183.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113270 restraints weight = 11291.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114723 restraints weight = 9214.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115642 restraints weight = 7997.144| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15330 Z= 0.131 Angle : 0.640 8.425 21012 Z= 0.309 Chirality : 0.043 0.240 2649 Planarity : 0.003 0.047 2469 Dihedral : 6.683 59.556 4021 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.98 % Favored : 94.66 % Rotamer: Outliers : 2.96 % Allowed : 15.74 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1668 helix: 1.02 (0.27), residues: 429 sheet: -0.18 (0.25), residues: 420 loop : -0.27 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 617 TYR 0.012 0.001 TYR D 486 PHE 0.026 0.001 PHE C 53 TRP 0.017 0.001 TRP C 112 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00299 (15186) covalent geometry : angle 0.60607 (20616) SS BOND : bond 0.00330 ( 36) SS BOND : angle 0.95287 ( 72) hydrogen bonds : bond 0.04343 ( 573) hydrogen bonds : angle 4.64084 ( 1557) link_ALPHA1-2 : bond 0.00390 ( 3) link_ALPHA1-2 : angle 2.09939 ( 9) link_ALPHA1-3 : bond 0.01333 ( 3) link_ALPHA1-3 : angle 0.78163 ( 9) link_ALPHA1-6 : bond 0.00415 ( 3) link_ALPHA1-6 : angle 1.53554 ( 9) link_BETA1-4 : bond 0.00493 ( 33) link_BETA1-4 : angle 1.59553 ( 99) link_BETA1-6 : bond 0.00380 ( 6) link_BETA1-6 : angle 1.14019 ( 18) link_NAG-ASN : bond 0.00307 ( 60) link_NAG-ASN : angle 1.85480 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.532 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 107 ASP cc_start: 0.8502 (m-30) cc_final: 0.8105 (t0) REVERT: A 166 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7730 (ttp80) REVERT: A 199 SER cc_start: 0.9542 (p) cc_final: 0.9105 (m) REVERT: A 207 LYS cc_start: 0.8584 (tppt) cc_final: 0.8030 (tmtt) REVERT: A 209 SER cc_start: 0.8793 (t) cc_final: 0.8367 (p) REVERT: B 616 ASN cc_start: 0.8484 (t0) cc_final: 0.7930 (p0) REVERT: B 620 SER cc_start: 0.8647 (m) cc_final: 0.8293 (t) REVERT: B 621 GLU cc_start: 0.8576 (tt0) cc_final: 0.8151 (tm-30) REVERT: C 125 LEU cc_start: 0.9234 (tp) cc_final: 0.8789 (tp) REVERT: C 199 SER cc_start: 0.9531 (p) cc_final: 0.9137 (m) REVERT: C 207 LYS cc_start: 0.8569 (tppt) cc_final: 0.7838 (tmtt) REVERT: C 209 SER cc_start: 0.8985 (t) cc_final: 0.8557 (p) REVERT: E 612 SER cc_start: 0.8868 (m) cc_final: 0.8512 (t) REVERT: E 616 ASN cc_start: 0.8630 (t0) cc_final: 0.8377 (t0) REVERT: D 103 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8509 (tm-30) REVERT: D 104 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8509 (ttm) REVERT: D 107 ASP cc_start: 0.8505 (m-30) cc_final: 0.8158 (t0) REVERT: D 125 LEU cc_start: 0.9198 (tp) cc_final: 0.8524 (tp) REVERT: D 199 SER cc_start: 0.9549 (p) cc_final: 0.9177 (m) REVERT: D 207 LYS cc_start: 0.8529 (tppt) cc_final: 0.8314 (mmtm) REVERT: D 209 SER cc_start: 0.8844 (t) cc_final: 0.8391 (p) REVERT: F 616 ASN cc_start: 0.8369 (t0) cc_final: 0.7695 (p0) REVERT: F 621 GLU cc_start: 0.8125 (tp30) cc_final: 0.7921 (tp30) outliers start: 45 outliers final: 40 residues processed: 221 average time/residue: 0.1062 time to fit residues: 35.7723 Evaluate side-chains 220 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 599 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 140 optimal weight: 0.0670 chunk 94 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109312 restraints weight = 23764.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112479 restraints weight = 15001.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114588 restraints weight = 11136.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116075 restraints weight = 9109.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116973 restraints weight = 7898.341| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15330 Z= 0.121 Angle : 0.623 6.386 21012 Z= 0.302 Chirality : 0.043 0.226 2649 Planarity : 0.003 0.044 2469 Dihedral : 6.194 51.911 4021 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.04 % Favored : 94.54 % Rotamer: Outliers : 3.16 % Allowed : 15.48 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1668 helix: 1.07 (0.27), residues: 429 sheet: -0.18 (0.24), residues: 420 loop : -0.25 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 166 TYR 0.014 0.001 TYR D 486 PHE 0.010 0.001 PHE A 383 TRP 0.015 0.001 TRP C 112 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00277 (15186) covalent geometry : angle 0.58960 (20616) SS BOND : bond 0.00294 ( 36) SS BOND : angle 0.87328 ( 72) hydrogen bonds : bond 0.04120 ( 573) hydrogen bonds : angle 4.59426 ( 1557) link_ALPHA1-2 : bond 0.00418 ( 3) link_ALPHA1-2 : angle 2.05774 ( 9) link_ALPHA1-3 : bond 0.01264 ( 3) link_ALPHA1-3 : angle 0.62793 ( 9) link_ALPHA1-6 : bond 0.00401 ( 3) link_ALPHA1-6 : angle 1.60667 ( 9) link_BETA1-4 : bond 0.00499 ( 33) link_BETA1-4 : angle 1.57619 ( 99) link_BETA1-6 : bond 0.00369 ( 6) link_BETA1-6 : angle 1.13822 ( 18) link_NAG-ASN : bond 0.00314 ( 60) link_NAG-ASN : angle 1.81389 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8505 (m-30) cc_final: 0.8082 (t0) REVERT: A 166 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7761 (ttp80) REVERT: A 199 SER cc_start: 0.9523 (p) cc_final: 0.9040 (m) REVERT: A 209 SER cc_start: 0.8737 (t) cc_final: 0.8291 (p) REVERT: B 616 ASN cc_start: 0.8465 (t0) cc_final: 0.7921 (p0) REVERT: B 621 GLU cc_start: 0.8515 (tt0) cc_final: 0.7627 (tm-30) REVERT: C 207 LYS cc_start: 0.8503 (tppt) cc_final: 0.7801 (tmtt) REVERT: C 209 SER cc_start: 0.8987 (t) cc_final: 0.8541 (p) REVERT: E 612 SER cc_start: 0.8850 (m) cc_final: 0.8396 (t) REVERT: E 616 ASN cc_start: 0.8552 (t0) cc_final: 0.8041 (p0) REVERT: D 103 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8533 (tm-30) REVERT: D 104 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8517 (ttm) REVERT: D 107 ASP cc_start: 0.8497 (m-30) cc_final: 0.8092 (t0) REVERT: D 199 SER cc_start: 0.9551 (p) cc_final: 0.9220 (m) REVERT: D 207 LYS cc_start: 0.8486 (tppt) cc_final: 0.7897 (tmtt) REVERT: D 209 SER cc_start: 0.8817 (t) cc_final: 0.8421 (p) REVERT: D 213 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8478 (tp) REVERT: F 571 TRP cc_start: 0.5209 (t60) cc_final: 0.4913 (t60) REVERT: F 616 ASN cc_start: 0.8361 (t0) cc_final: 0.7761 (p0) outliers start: 48 outliers final: 42 residues processed: 222 average time/residue: 0.1033 time to fit residues: 35.0806 Evaluate side-chains 223 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 118 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.130706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108641 restraints weight = 23940.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111852 restraints weight = 15228.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113941 restraints weight = 11317.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115438 restraints weight = 9271.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116403 restraints weight = 8044.038| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15330 Z= 0.134 Angle : 0.636 9.062 21012 Z= 0.308 Chirality : 0.044 0.352 2649 Planarity : 0.003 0.040 2469 Dihedral : 6.098 46.958 4021 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.04 % Favored : 94.54 % Rotamer: Outliers : 3.23 % Allowed : 15.74 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1668 helix: 1.13 (0.27), residues: 429 sheet: -0.19 (0.25), residues: 420 loop : -0.27 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 166 TYR 0.022 0.001 TYR D 486 PHE 0.027 0.002 PHE C 53 TRP 0.027 0.001 TRP E 596 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00311 (15186) covalent geometry : angle 0.60012 (20616) SS BOND : bond 0.00322 ( 36) SS BOND : angle 0.88588 ( 72) hydrogen bonds : bond 0.04152 ( 573) hydrogen bonds : angle 4.57889 ( 1557) link_ALPHA1-2 : bond 0.00438 ( 3) link_ALPHA1-2 : angle 1.99490 ( 9) link_ALPHA1-3 : bond 0.01220 ( 3) link_ALPHA1-3 : angle 0.68511 ( 9) link_ALPHA1-6 : bond 0.00391 ( 3) link_ALPHA1-6 : angle 1.56204 ( 9) link_BETA1-4 : bond 0.00487 ( 33) link_BETA1-4 : angle 1.58790 ( 99) link_BETA1-6 : bond 0.00359 ( 6) link_BETA1-6 : angle 1.13819 ( 18) link_NAG-ASN : bond 0.00308 ( 60) link_NAG-ASN : angle 1.95647 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.547 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 107 ASP cc_start: 0.8509 (m-30) cc_final: 0.8153 (t0) REVERT: A 112 TRP cc_start: 0.8771 (t-100) cc_final: 0.8466 (t-100) REVERT: A 166 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7771 (ttp80) REVERT: A 207 LYS cc_start: 0.8487 (tppt) cc_final: 0.7891 (tmtt) REVERT: A 209 SER cc_start: 0.8765 (t) cc_final: 0.8379 (p) REVERT: B 616 ASN cc_start: 0.8499 (t0) cc_final: 0.7963 (p0) REVERT: B 621 GLU cc_start: 0.8540 (tt0) cc_final: 0.8155 (tm-30) REVERT: C 125 LEU cc_start: 0.9223 (tp) cc_final: 0.8774 (tp) REVERT: C 207 LYS cc_start: 0.8524 (tppt) cc_final: 0.7801 (tmtt) REVERT: C 209 SER cc_start: 0.8963 (t) cc_final: 0.8577 (p) REVERT: E 612 SER cc_start: 0.8954 (m) cc_final: 0.8548 (t) REVERT: E 616 ASN cc_start: 0.8521 (t0) cc_final: 0.7971 (p0) REVERT: D 103 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8523 (tm-30) REVERT: D 104 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8527 (ttm) REVERT: D 107 ASP cc_start: 0.8484 (m-30) cc_final: 0.8090 (t0) REVERT: D 209 SER cc_start: 0.8822 (t) cc_final: 0.8360 (p) REVERT: D 213 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8520 (tp) REVERT: D 249 HIS cc_start: 0.7425 (p-80) cc_final: 0.7016 (p-80) REVERT: F 571 TRP cc_start: 0.5357 (t60) cc_final: 0.5120 (t60) REVERT: F 616 ASN cc_start: 0.8370 (t0) cc_final: 0.7739 (p0) outliers start: 49 outliers final: 41 residues processed: 218 average time/residue: 0.1075 time to fit residues: 35.3438 Evaluate side-chains 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108040 restraints weight = 23760.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111099 restraints weight = 15172.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113241 restraints weight = 11396.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114704 restraints weight = 9322.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115612 restraints weight = 8074.965| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15330 Z= 0.140 Angle : 0.635 7.078 21012 Z= 0.308 Chirality : 0.043 0.298 2649 Planarity : 0.004 0.045 2469 Dihedral : 6.002 44.413 4019 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.22 % Favored : 94.36 % Rotamer: Outliers : 3.03 % Allowed : 15.55 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.21), residues: 1668 helix: 1.10 (0.27), residues: 438 sheet: -0.28 (0.24), residues: 444 loop : -0.30 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 166 TYR 0.019 0.001 TYR D 486 PHE 0.011 0.001 PHE D 383 TRP 0.023 0.001 TRP E 596 HIS 0.002 0.001 HIS E 564 Details of bonding type rmsd covalent geometry : bond 0.00323 (15186) covalent geometry : angle 0.59962 (20616) SS BOND : bond 0.00345 ( 36) SS BOND : angle 0.90369 ( 72) hydrogen bonds : bond 0.04180 ( 573) hydrogen bonds : angle 4.59258 ( 1557) link_ALPHA1-2 : bond 0.00441 ( 3) link_ALPHA1-2 : angle 1.96412 ( 9) link_ALPHA1-3 : bond 0.01144 ( 3) link_ALPHA1-3 : angle 0.73863 ( 9) link_ALPHA1-6 : bond 0.00402 ( 3) link_ALPHA1-6 : angle 1.55196 ( 9) link_BETA1-4 : bond 0.00476 ( 33) link_BETA1-4 : angle 1.59255 ( 99) link_BETA1-6 : bond 0.00359 ( 6) link_BETA1-6 : angle 1.12501 ( 18) link_NAG-ASN : bond 0.00296 ( 60) link_NAG-ASN : angle 1.91332 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.33 seconds wall clock time: 35 minutes 16.48 seconds (2116.48 seconds total)