Starting phenix.real_space_refine on Sat Sep 12 10:02:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6v0r_20396/09_2026/6v0r_20396.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0r_20396/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6v0r_20396/09_2026/6v0r_20396.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6v0r_20396/09_2026/6v0r_20396.cif" model { file = "/net/cci-nas-00/data/ceres_data/6v0r_20396/09_2026/6v0r_20396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0r_20396/09_2026/6v0r_20396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v0r_20396/09_2026/6v0r_20396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0r_20396/09_2026/6v0r_20396.map" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 3.58, per 1000 atoms: 0.24 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: 1.59 Conformation dependent library (CDL) restraints added in 597.0 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: 0.61 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: 2.60 Time building geometry restraints manager: 2.06 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 - 16.99: 7914 16.99 - 33.97: 264 33.97 - 50.96: 105 50.96 - 67.94: 42 67.94 - 84.93: 6 Dihedral angle restraints: 8331 sinusoidal: 3411 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 8328 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: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.130 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 : 10.969 84.927 5031 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/Z covalent geometry : bond 0.01982 / 1.05 (15186) covalent geometry : angle 1.79986 / 1.11 (20616) SS BOND : bond 0.23056 / 13.91 ( 36) SS BOND : angle 7.90907 / 5.67 ( 72) hydrogen bonds : bond 0.18370 / 12.14 ( 573) hydrogen bonds : angle 7.15498 / 5.07 ( 1557) link_ALPHA1-2 : bond 0.03745 / 1.67 ( 3) link_ALPHA1-2 : angle 2.67659 / 1.64 ( 9) link_ALPHA1-3 : bond 0.03424 / 1.53 ( 3) link_ALPHA1-3 : angle 2.51662 / 1.55 ( 9) link_ALPHA1-6 : bond 0.03692 / 1.65 ( 3) link_ALPHA1-6 : angle 3.19547 / 1.98 ( 9) link_BETA1-4 : bond 0.02831 / 1.81 ( 33) link_BETA1-4 : angle 3.80013 / 2.68 ( 99) link_BETA1-6 : bond 0.01700 / 0.98 ( 6) link_BETA1-6 : angle 4.66855 / 2.99 ( 18) link_NAG-ASN : bond 0.03061 / 1.96 ( 60) link_NAG-ASN : angle 2.32995 / 1.62 ( 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 : 0.539 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: 0.1245 time to fit residues: 73.7589 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 : 0.537 ------------------------------------------------------------------------------- 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... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106955 restraints weight = 22325.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108388 restraints weight = 17923.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109453 restraints weight = 15368.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110111 restraints weight = 13634.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110438 restraints weight = 12598.444| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15330 Z= 0.185 Angle : 0.843 10.073 21012 Z= 0.418 Chirality : 0.045 0.160 2649 Planarity : 0.004 0.031 2469 Dihedral : 6.446 54.613 1826 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.62 % Favored : 95.02 % Rotamer: Outliers : 2.50 % Allowed : 9.62 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.21), residues: 1668 helix: 0.82 (0.27), residues: 387 sheet: 0.29 (0.24), residues: 465 loop : 0.60 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 579 TYR 0.016 0.002 TYR A 484 PHE 0.020 0.002 PHE C 383 TRP 0.015 0.002 TRP F 623 HIS 0.006 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (15186) covalent geometry : angle 0.79210 / 0.41 (20616) SS BOND : bond 0.00491 / 0.29 ( 36) SS BOND : angle 1.71708 / 1.21 ( 72) hydrogen bonds : bond 0.06695 / 4.48 ( 573) hydrogen bonds : angle 5.63386 / 3.92 ( 1557) link_ALPHA1-2 : bond 0.00693 / 0.31 ( 3) link_ALPHA1-2 : angle 1.33485 / 0.73 ( 9) link_ALPHA1-3 : bond 0.00616 / 0.27 ( 3) link_ALPHA1-3 : angle 1.60185 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00791 / 0.35 ( 3) link_ALPHA1-6 : angle 1.26913 / 0.69 ( 9) link_BETA1-4 : bond 0.00437 / 0.28 ( 33) link_BETA1-4 : angle 2.26316 / 1.58 ( 99) link_BETA1-6 : bond 0.00545 / 0.30 ( 6) link_BETA1-6 : angle 1.20373 / 0.77 ( 18) link_NAG-ASN : bond 0.00381 / 0.24 ( 60) link_NAG-ASN : angle 2.57081 / 1.74 ( 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 268 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9282 (p) cc_final: 0.9065 (m) REVERT: B 530 MET cc_start: 0.8172 (mtp) cc_final: 0.7776 (mtp) REVERT: B 535 MET cc_start: 0.8648 (mmt) cc_final: 0.8339 (mpp) REVERT: B 543 ASN cc_start: 0.8600 (m-40) cc_final: 0.8251 (m-40) REVERT: B 612 SER cc_start: 0.7687 (p) cc_final: 0.7301 (t) REVERT: B 616 ASN cc_start: 0.7994 (t0) cc_final: 0.7396 (p0) REVERT: C 125 LEU cc_start: 0.9198 (tp) cc_final: 0.8602 (tp) REVERT: C 199 SER cc_start: 0.9272 (p) cc_final: 0.8943 (m) REVERT: C 452 LEU cc_start: 0.9112 (mt) cc_final: 0.8900 (mp) REVERT: C 474 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7406 (p0) REVERT: E 612 SER cc_start: 0.8083 (p) cc_final: 0.7759 (t) REVERT: E 616 ASN cc_start: 0.7884 (t0) cc_final: 0.7293 (p0) REVERT: D 199 SER cc_start: 0.9364 (p) cc_final: 0.9022 (m) REVERT: D 502 LYS cc_start: 0.8287 (tttm) cc_final: 0.8040 (tttt) REVERT: F 530 MET cc_start: 0.7839 (mtp) cc_final: 0.7354 (mtp) REVERT: F 543 ASN cc_start: 0.8478 (m-40) cc_final: 0.8115 (m-40) REVERT: F 612 SER cc_start: 0.7948 (p) cc_final: 0.7538 (t) REVERT: F 616 ASN cc_start: 0.7780 (t0) cc_final: 0.7188 (p0) outliers start: 38 outliers final: 25 residues processed: 254 average time/residue: 0.1202 time to fit residues: 45.8561 Evaluate side-chains 194 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 E residue 663 LEU Chi-restraints excluded: chain D residue 75 VAL 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 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: 2.9990 chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.081008 restraints weight = 24523.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.082827 restraints weight = 18461.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.083964 restraints weight = 15204.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.084951 restraints weight = 13297.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.085553 restraints weight = 12054.639| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15330 Z= 0.225 Angle : 0.776 9.866 21012 Z= 0.386 Chirality : 0.045 0.158 2649 Planarity : 0.004 0.040 2469 Dihedral : 6.109 52.195 1818 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.28 % Favored : 94.36 % Rotamer: Outliers : 3.56 % Allowed : 11.07 % Favored : 85.38 % 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: 0.39 (0.20), residues: 1668 helix: 0.82 (0.27), residues: 402 sheet: -0.09 (0.24), residues: 417 loop : 0.34 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 617 TYR 0.016 0.002 TYR A 484 PHE 0.018 0.003 PHE D 176 TRP 0.016 0.002 TRP F 623 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (15186) covalent geometry : angle 0.73992 / 0.38 (20616) SS BOND : bond 0.00651 / 0.39 ( 36) SS BOND : angle 1.56126 / 1.12 ( 72) hydrogen bonds : bond 0.05954 / 3.95 ( 573) hydrogen bonds : angle 5.22787 / 3.61 ( 1557) link_ALPHA1-2 : bond 0.00605 / 0.27 ( 3) link_ALPHA1-2 : angle 1.65574 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00701 / 0.31 ( 3) link_ALPHA1-3 : angle 1.12257 / 0.61 ( 9) link_ALPHA1-6 : bond 0.00660 / 0.29 ( 3) link_ALPHA1-6 : angle 1.30241 / 0.69 ( 9) link_BETA1-4 : bond 0.00460 / 0.30 ( 33) link_BETA1-4 : angle 1.63650 / 1.14 ( 99) link_BETA1-6 : bond 0.00300 / 0.17 ( 6) link_BETA1-6 : angle 1.08156 / 0.66 ( 18) link_NAG-ASN : bond 0.00410 / 0.26 ( 60) link_NAG-ASN : angle 2.17635 / 1.47 ( 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 243 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9376 (p) cc_final: 0.9070 (m) REVERT: B 612 SER cc_start: 0.8288 (p) cc_final: 0.8010 (t) REVERT: B 616 ASN cc_start: 0.8175 (t0) cc_final: 0.7502 (p0) REVERT: C 199 SER cc_start: 0.9406 (p) cc_final: 0.8946 (m) REVERT: E 542 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8279 (ttp-170) REVERT: E 616 ASN cc_start: 0.8080 (t0) cc_final: 0.7318 (p0) REVERT: D 199 SER cc_start: 0.9446 (p) cc_final: 0.8933 (m) REVERT: D 271 MET cc_start: 0.7725 (mtp) cc_final: 0.7472 (mtm) REVERT: F 543 ASN cc_start: 0.8555 (m-40) cc_final: 0.8166 (m-40) REVERT: F 616 ASN cc_start: 0.8148 (t0) cc_final: 0.7459 (p0) REVERT: F 647 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6744 (mt-10) outliers start: 54 outliers final: 39 residues processed: 221 average time/residue: 0.1114 time to fit residues: 37.8026 Evaluate side-chains 210 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 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 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 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 576 LEU Chi-restraints excluded: chain D residue 47 ASP 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 373 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 467 THR 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: 0.6980 chunk 155 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** 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 = 0.3694 r_free = 0.3694 target = 0.130065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107889 restraints weight = 23380.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111118 restraints weight = 14727.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113319 restraints weight = 10917.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114778 restraints weight = 8889.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115775 restraints weight = 7701.647| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15330 Z= 0.180 Angle : 0.699 7.868 21012 Z= 0.343 Chirality : 0.043 0.166 2649 Planarity : 0.004 0.041 2469 Dihedral : 5.822 48.921 1815 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.44 % Favored : 95.20 % Rotamer: Outliers : 3.82 % Allowed : 12.45 % Favored : 83.73 % 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: 0.23 (0.21), residues: 1668 helix: 0.66 (0.27), residues: 429 sheet: -0.13 (0.24), residues: 417 loop : 0.20 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 166 TYR 0.011 0.001 TYR A 484 PHE 0.014 0.002 PHE D 383 TRP 0.020 0.001 TRP F 623 HIS 0.004 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (15186) covalent geometry : angle 0.66625 / 0.34 (20616) SS BOND : bond 0.00511 / 0.30 ( 36) SS BOND : angle 1.20491 / 0.86 ( 72) hydrogen bonds : bond 0.05207 / 3.45 ( 573) hydrogen bonds : angle 5.01780 / 3.46 ( 1557) link_ALPHA1-2 : bond 0.00553 / 0.25 ( 3) link_ALPHA1-2 : angle 1.65571 / 0.89 ( 9) link_ALPHA1-3 : bond 0.00571 / 0.25 ( 3) link_ALPHA1-3 : angle 1.17895 / 0.64 ( 9) link_ALPHA1-6 : bond 0.00537 / 0.24 ( 3) link_ALPHA1-6 : angle 1.36368 / 0.74 ( 9) link_BETA1-4 : bond 0.00387 / 0.25 ( 33) link_BETA1-4 : angle 1.40299 / 0.98 ( 99) link_BETA1-6 : bond 0.00343 / 0.20 ( 6) link_BETA1-6 : angle 0.99087 / 0.59 ( 18) link_NAG-ASN : bond 0.00351 / 0.23 ( 60) link_NAG-ASN : angle 2.02849 / 1.37 ( 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 234 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7875 (ttp80) REVERT: A 199 SER cc_start: 0.9462 (p) cc_final: 0.9182 (m) REVERT: A 271 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7258 (mtp) REVERT: B 543 ASN cc_start: 0.8705 (m110) cc_final: 0.8484 (m-40) REVERT: B 612 SER cc_start: 0.8642 (p) cc_final: 0.8346 (t) REVERT: B 616 ASN cc_start: 0.8386 (t0) cc_final: 0.7664 (p0) REVERT: C 125 LEU cc_start: 0.9281 (tp) cc_final: 0.8658 (tp) REVERT: C 199 SER cc_start: 0.9464 (p) cc_final: 0.8960 (m) REVERT: E 612 SER cc_start: 0.8515 (m) cc_final: 0.8052 (t) REVERT: E 616 ASN cc_start: 0.8342 (t0) cc_final: 0.7627 (p0) REVERT: E 647 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6920 (mt-10) REVERT: D 199 SER cc_start: 0.9476 (p) cc_final: 0.9076 (m) REVERT: D 207 LYS cc_start: 0.8752 (tppt) cc_final: 0.8450 (mmtm) REVERT: D 271 MET cc_start: 0.7704 (mtp) cc_final: 0.7353 (mtm) REVERT: F 616 ASN cc_start: 0.8412 (t0) cc_final: 0.7569 (p0) REVERT: F 647 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6901 (mt-10) outliers start: 58 outliers final: 42 residues processed: 215 average time/residue: 0.1112 time to fit residues: 36.8387 Evaluate side-chains 207 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 234 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 271 MET 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 627 THR 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 365 SER Chi-restraints excluded: chain C residue 467 THR 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 576 LEU Chi-restraints excluded: chain E residue 653 GLN Chi-restraints excluded: chain D residue 47 ASP 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 265 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 467 THR 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: 5.9990 chunk 7 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** E 625 ASN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104922 restraints weight = 23816.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108044 restraints weight = 15107.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110180 restraints weight = 11314.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111606 restraints weight = 9261.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112510 restraints weight = 8046.777| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15330 Z= 0.205 Angle : 0.702 7.792 21012 Z= 0.345 Chirality : 0.044 0.176 2649 Planarity : 0.004 0.045 2469 Dihedral : 5.702 48.228 1815 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.12 % Favored : 93.53 % Rotamer: Outliers : 3.89 % Allowed : 12.85 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1668 helix: 0.92 (0.27), residues: 411 sheet: -0.34 (0.25), residues: 420 loop : 0.02 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 166 TYR 0.011 0.002 TYR A 484 PHE 0.015 0.002 PHE D 383 TRP 0.014 0.002 TRP F 623 HIS 0.003 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (15186) covalent geometry : angle 0.67200 / 0.34 (20616) SS BOND : bond 0.00549 / 0.33 ( 36) SS BOND : angle 1.19587 / 0.86 ( 72) hydrogen bonds : bond 0.05193 / 3.44 ( 573) hydrogen bonds : angle 4.90308 / 3.37 ( 1557) link_ALPHA1-2 : bond 0.00451 / 0.20 ( 3) link_ALPHA1-2 : angle 1.77549 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00559 / 0.25 ( 3) link_ALPHA1-3 : angle 1.14285 / 0.65 ( 9) link_ALPHA1-6 : bond 0.00437 / 0.20 ( 3) link_ALPHA1-6 : angle 1.36826 / 0.74 ( 9) link_BETA1-4 : bond 0.00358 / 0.23 ( 33) link_BETA1-4 : angle 1.34077 / 0.93 ( 99) link_BETA1-6 : bond 0.00323 / 0.18 ( 6) link_BETA1-6 : angle 1.05160 / 0.63 ( 18) link_NAG-ASN : bond 0.00362 / 0.24 ( 60) link_NAG-ASN : angle 1.96499 / 1.33 ( 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 243 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.566 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 114 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 166 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7751 (ttp80) REVERT: A 199 SER cc_start: 0.9538 (p) cc_final: 0.9227 (m) REVERT: A 271 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7284 (mtp) REVERT: B 612 SER cc_start: 0.8764 (p) cc_final: 0.8550 (t) REVERT: B 616 ASN cc_start: 0.8535 (t0) cc_final: 0.7840 (p0) REVERT: B 647 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6968 (mt-10) REVERT: C 125 LEU cc_start: 0.9301 (tp) cc_final: 0.8730 (tp) REVERT: C 199 SER cc_start: 0.9531 (p) cc_final: 0.9210 (m) REVERT: C 207 LYS cc_start: 0.8675 (tppt) cc_final: 0.7874 (tmtt) REVERT: C 467 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8266 (p) REVERT: E 612 SER cc_start: 0.8808 (m) cc_final: 0.8390 (t) REVERT: E 616 ASN cc_start: 0.8547 (t0) cc_final: 0.7843 (p0) REVERT: D 114 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8111 (tm-30) REVERT: D 125 LEU cc_start: 0.9159 (tp) cc_final: 0.8492 (tp) REVERT: D 199 SER cc_start: 0.9525 (p) cc_final: 0.9186 (m) REVERT: D 207 LYS cc_start: 0.8717 (tppt) cc_final: 0.8423 (mmtm) REVERT: D 209 SER cc_start: 0.8812 (t) cc_final: 0.8316 (p) REVERT: D 271 MET cc_start: 0.7746 (mtp) cc_final: 0.7400 (mtm) REVERT: D 466 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: F 530 MET cc_start: 0.8526 (ttm) cc_final: 0.8305 (ttm) REVERT: F 634 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7423 (tm-30) outliers start: 59 outliers final: 45 residues processed: 226 average time/residue: 0.1116 time to fit residues: 38.5377 Evaluate side-chains 214 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 90 THR 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 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 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 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 365 SER Chi-restraints excluded: chain C residue 467 THR 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 576 LEU Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 627 THR Chi-restraints excluded: chain E residue 663 LEU 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 373 THR Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 467 THR 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 545 LEU Chi-restraints excluded: chain F residue 625 ASN 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: 0.7980 chunk 124 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 246 GLN E 625 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108240 restraints weight = 23307.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111483 restraints weight = 14802.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113631 restraints weight = 10956.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115014 restraints weight = 8963.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116020 restraints weight = 7803.987| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15330 Z= 0.127 Angle : 0.631 7.167 21012 Z= 0.309 Chirality : 0.042 0.172 2649 Planarity : 0.004 0.038 2469 Dihedral : 5.458 47.765 1815 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.74 % Favored : 94.90 % Rotamer: Outliers : 3.29 % Allowed : 14.36 % Favored : 82.35 % 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: 0.09 (0.21), residues: 1668 helix: 0.85 (0.27), residues: 429 sheet: -0.28 (0.25), residues: 420 loop : -0.04 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 166 TYR 0.007 0.001 TYR A 484 PHE 0.011 0.001 PHE D 383 TRP 0.012 0.001 TRP F 623 HIS 0.003 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15186) covalent geometry : angle 0.60255 / 0.30 (20616) SS BOND : bond 0.00356 / 0.21 ( 36) SS BOND : angle 0.97050 / 0.69 ( 72) hydrogen bonds : bond 0.04541 / 3.02 ( 573) hydrogen bonds : angle 4.72049 / 3.25 ( 1557) link_ALPHA1-2 : bond 0.00492 / 0.22 ( 3) link_ALPHA1-2 : angle 1.75777 / 0.95 ( 9) link_ALPHA1-3 : bond 0.00643 / 0.28 ( 3) link_ALPHA1-3 : angle 1.14640 / 0.63 ( 9) link_ALPHA1-6 : bond 0.00385 / 0.18 ( 3) link_ALPHA1-6 : angle 1.36784 / 0.75 ( 9) link_BETA1-4 : bond 0.00395 / 0.26 ( 33) link_BETA1-4 : angle 1.19440 / 0.84 ( 99) link_BETA1-6 : bond 0.00411 / 0.24 ( 6) link_BETA1-6 : angle 1.05402 / 0.61 ( 18) link_NAG-ASN : bond 0.00306 / 0.20 ( 60) link_NAG-ASN : angle 1.82997 / 1.24 ( 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 244 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8239 (tm-30) REVERT: A 166 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7677 (ttp80) REVERT: A 199 SER cc_start: 0.9520 (p) cc_final: 0.9221 (m) REVERT: A 207 LYS cc_start: 0.8695 (tppt) cc_final: 0.8378 (mttp) REVERT: A 209 SER cc_start: 0.8770 (t) cc_final: 0.8366 (p) REVERT: A 271 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7247 (mtp) REVERT: A 486 TYR cc_start: 0.8942 (m-80) cc_final: 0.8511 (m-10) REVERT: B 612 SER cc_start: 0.8731 (p) cc_final: 0.8503 (t) REVERT: B 616 ASN cc_start: 0.8481 (t0) cc_final: 0.7840 (p0) REVERT: C 199 SER cc_start: 0.9536 (p) cc_final: 0.9002 (m) REVERT: C 207 LYS cc_start: 0.8578 (tppt) cc_final: 0.7803 (tmtt) REVERT: C 467 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8125 (p) REVERT: E 612 SER cc_start: 0.8781 (m) cc_final: 0.8345 (t) REVERT: E 616 ASN cc_start: 0.8500 (t0) cc_final: 0.7811 (p0) REVERT: E 647 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6755 (mt-10) REVERT: D 103 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8404 (tm-30) REVERT: D 114 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 199 SER cc_start: 0.9519 (p) cc_final: 0.9193 (m) REVERT: D 207 LYS cc_start: 0.8666 (tppt) cc_final: 0.8430 (mmtm) REVERT: D 209 SER cc_start: 0.8808 (t) cc_final: 0.8314 (p) REVERT: D 340 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7518 (tm-30) REVERT: F 565 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7888 (pp) REVERT: F 571 TRP cc_start: 0.5483 (t60) cc_final: 0.5112 (t60) REVERT: F 621 GLU cc_start: 0.8321 (tp30) cc_final: 0.8120 (tp30) REVERT: F 634 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7373 (tm-30) outliers start: 50 outliers final: 36 residues processed: 226 average time/residue: 0.1195 time to fit residues: 41.0057 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 : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 365 SER 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 625 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 109 ILE 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 467 THR Chi-restraints excluded: chain C residue 474 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 627 THR Chi-restraints excluded: chain E residue 663 LEU 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 466 GLU Chi-restraints excluded: chain D residue 467 THR 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 545 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 663 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 287 GLN ** 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 478 ASN F 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.104286 restraints weight = 23609.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107361 restraints weight = 15198.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109453 restraints weight = 11405.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110854 restraints weight = 9372.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111764 restraints weight = 8177.026| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15330 Z= 0.218 Angle : 0.699 8.330 21012 Z= 0.341 Chirality : 0.044 0.290 2649 Planarity : 0.004 0.044 2469 Dihedral : 5.329 48.886 1813 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.82 % Favored : 93.82 % Rotamer: Outliers : 4.08 % Allowed : 13.77 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1668 helix: 0.94 (0.27), residues: 429 sheet: -0.38 (0.25), residues: 417 loop : -0.23 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 166 TYR 0.010 0.001 TYR C 484 PHE 0.016 0.002 PHE D 383 TRP 0.012 0.002 TRP E 596 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (15186) covalent geometry : angle 0.66962 / 0.34 (20616) SS BOND : bond 0.00520 / 0.31 ( 36) SS BOND : angle 1.07595 / 0.76 ( 72) hydrogen bonds : bond 0.04992 / 3.31 ( 573) hydrogen bonds : angle 4.76607 / 3.28 ( 1557) link_ALPHA1-2 : bond 0.00428 / 0.19 ( 3) link_ALPHA1-2 : angle 1.78455 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00583 / 0.25 ( 3) link_ALPHA1-3 : angle 1.13498 / 0.63 ( 9) link_ALPHA1-6 : bond 0.00278 / 0.12 ( 3) link_ALPHA1-6 : angle 1.39171 / 0.77 ( 9) link_BETA1-4 : bond 0.00355 / 0.23 ( 33) link_BETA1-4 : angle 1.30918 / 0.90 ( 99) link_BETA1-6 : bond 0.00311 / 0.18 ( 6) link_BETA1-6 : angle 1.06042 / 0.63 ( 18) link_NAG-ASN : bond 0.00367 / 0.24 ( 60) link_NAG-ASN : angle 1.96811 / 1.33 ( 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 241 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8039 (tm-30) REVERT: A 166 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7729 (ttp80) REVERT: A 199 SER cc_start: 0.9580 (p) cc_final: 0.9020 (m) REVERT: A 209 SER cc_start: 0.8825 (t) cc_final: 0.8457 (p) REVERT: A 271 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7303 (mtp) REVERT: B 616 ASN cc_start: 0.8591 (t0) cc_final: 0.7852 (p0) REVERT: B 647 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6858 (mt-10) REVERT: C 125 LEU cc_start: 0.9295 (tp) cc_final: 0.8748 (tp) REVERT: C 199 SER cc_start: 0.9515 (p) cc_final: 0.9114 (m) REVERT: C 207 LYS cc_start: 0.8526 (tppt) cc_final: 0.7782 (tmtt) REVERT: E 612 SER cc_start: 0.8920 (m) cc_final: 0.8553 (t) REVERT: E 616 ASN cc_start: 0.8645 (t0) cc_final: 0.8389 (t0) REVERT: D 125 LEU cc_start: 0.9213 (tp) cc_final: 0.8631 (tp) REVERT: D 199 SER cc_start: 0.9540 (p) cc_final: 0.9234 (m) REVERT: D 207 LYS cc_start: 0.8751 (tppt) cc_final: 0.8447 (mmtm) REVERT: D 209 SER cc_start: 0.8852 (t) cc_final: 0.8414 (p) REVERT: D 213 ILE cc_start: 0.8535 (tp) cc_final: 0.8036 (pt) REVERT: F 634 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7270 (tm-30) outliers start: 62 outliers final: 46 residues processed: 225 average time/residue: 0.1143 time to fit residues: 39.4948 Evaluate side-chains 219 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 90 THR 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 365 SER 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 625 ASN 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 109 ILE 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 627 THR Chi-restraints excluded: chain E residue 641 ILE 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 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 373 THR 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 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 599 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 150 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN F 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103576 restraints weight = 24213.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106597 restraints weight = 15614.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108630 restraints weight = 11764.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110000 restraints weight = 9723.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110976 restraints weight = 8503.440| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15330 Z= 0.210 Angle : 0.703 7.785 21012 Z= 0.344 Chirality : 0.044 0.240 2649 Planarity : 0.004 0.044 2469 Dihedral : 5.367 50.005 1813 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.64 % Favored : 94.00 % Rotamer: Outliers : 4.08 % Allowed : 13.44 % Favored : 82.48 % 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 (0.20), residues: 1668 helix: 0.98 (0.27), residues: 429 sheet: -0.52 (0.25), residues: 417 loop : -0.33 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.009 0.001 TYR A 484 PHE 0.015 0.002 PHE D 383 TRP 0.012 0.002 TRP A 45 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (15186) covalent geometry : angle 0.67384 / 0.34 (20616) SS BOND : bond 0.00535 / 0.33 ( 36) SS BOND : angle 1.19967 / 0.85 ( 72) hydrogen bonds : bond 0.05028 / 3.35 ( 573) hydrogen bonds : angle 4.78554 / 3.29 ( 1557) link_ALPHA1-2 : bond 0.00402 / 0.18 ( 3) link_ALPHA1-2 : angle 1.83178 / 0.99 ( 9) link_ALPHA1-3 : bond 0.00588 / 0.26 ( 3) link_ALPHA1-3 : angle 1.12338 / 0.61 ( 9) link_ALPHA1-6 : bond 0.00307 / 0.14 ( 3) link_ALPHA1-6 : angle 1.38285 / 0.76 ( 9) link_BETA1-4 : bond 0.00354 / 0.23 ( 33) link_BETA1-4 : angle 1.27161 / 0.89 ( 99) link_BETA1-6 : bond 0.00366 / 0.21 ( 6) link_BETA1-6 : angle 1.06990 / 0.63 ( 18) link_NAG-ASN : bond 0.00368 / 0.24 ( 60) link_NAG-ASN : angle 1.94615 / 1.32 ( 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 237 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8665 (ttp) cc_final: 0.8285 (ttm) REVERT: A 114 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8118 (tm-30) REVERT: A 209 SER cc_start: 0.8855 (t) cc_final: 0.8471 (p) REVERT: A 271 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7289 (mtp) REVERT: C 125 LEU cc_start: 0.9316 (tp) cc_final: 0.8790 (tp) REVERT: C 207 LYS cc_start: 0.8710 (tppt) cc_final: 0.7888 (tmtt) REVERT: E 542 ARG cc_start: 0.8706 (ttp-170) cc_final: 0.8464 (mtm-85) REVERT: E 612 SER cc_start: 0.9034 (m) cc_final: 0.8732 (t) REVERT: E 616 ASN cc_start: 0.8675 (t0) cc_final: 0.8456 (t0) REVERT: D 104 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8318 (ttm) REVERT: D 125 LEU cc_start: 0.9223 (tp) cc_final: 0.8645 (tp) REVERT: D 209 SER cc_start: 0.8904 (t) cc_final: 0.8545 (p) REVERT: F 634 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7373 (tm-30) outliers start: 62 outliers final: 50 residues processed: 219 average time/residue: 0.1123 time to fit residues: 37.6435 Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 90 THR 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 257 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 346 VAL 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 625 ASN 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 109 ILE 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 576 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 90 THR Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 115 SER 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 346 VAL Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 625 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN F 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.127184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105181 restraints weight = 24115.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108247 restraints weight = 15500.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110321 restraints weight = 11623.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111720 restraints weight = 9581.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112669 restraints weight = 8366.313| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15330 Z= 0.155 Angle : 0.665 7.476 21012 Z= 0.325 Chirality : 0.043 0.239 2649 Planarity : 0.004 0.041 2469 Dihedral : 5.268 49.398 1813 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.46 % Favored : 94.18 % Rotamer: Outliers : 3.36 % Allowed : 14.03 % Favored : 82.61 % 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: -0.07 (0.21), residues: 1668 helix: 1.08 (0.27), residues: 429 sheet: -0.35 (0.26), residues: 393 loop : -0.40 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 166 TYR 0.008 0.001 TYR A 217 PHE 0.026 0.002 PHE C 53 TRP 0.014 0.001 TRP F 623 HIS 0.003 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (15186) covalent geometry : angle 0.63569 / 0.32 (20616) SS BOND : bond 0.00429 / 0.25 ( 36) SS BOND : angle 1.15362 / 0.81 ( 72) hydrogen bonds : bond 0.04698 / 3.13 ( 573) hydrogen bonds : angle 4.74014 / 3.26 ( 1557) link_ALPHA1-2 : bond 0.00429 / 0.19 ( 3) link_ALPHA1-2 : angle 1.81154 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00659 / 0.29 ( 3) link_ALPHA1-3 : angle 1.09407 / 0.59 ( 9) link_ALPHA1-6 : bond 0.00313 / 0.14 ( 3) link_ALPHA1-6 : angle 1.40080 / 0.77 ( 9) link_BETA1-4 : bond 0.00366 / 0.24 ( 33) link_BETA1-4 : angle 1.21732 / 0.85 ( 99) link_BETA1-6 : bond 0.00397 / 0.23 ( 6) link_BETA1-6 : angle 1.06382 / 0.62 ( 18) link_NAG-ASN : bond 0.00328 / 0.22 ( 60) link_NAG-ASN : angle 1.88608 / 1.28 ( 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 227 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8796 (t-100) cc_final: 0.8489 (t-100) REVERT: A 114 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 209 SER cc_start: 0.8849 (t) cc_final: 0.8461 (p) REVERT: A 271 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7226 (mtp) REVERT: B 621 GLU cc_start: 0.8492 (tt0) cc_final: 0.7744 (tp30) REVERT: C 107 ASP cc_start: 0.8393 (m-30) cc_final: 0.8047 (t0) REVERT: C 125 LEU cc_start: 0.9301 (tp) cc_final: 0.8764 (tp) REVERT: C 207 LYS cc_start: 0.8635 (tppt) cc_final: 0.7877 (tmtt) REVERT: E 612 SER cc_start: 0.9030 (m) cc_final: 0.8718 (t) REVERT: E 616 ASN cc_start: 0.8707 (t0) cc_final: 0.8468 (t0) REVERT: D 125 LEU cc_start: 0.9215 (tp) cc_final: 0.8705 (tp) REVERT: D 209 SER cc_start: 0.8905 (t) cc_final: 0.8557 (p) REVERT: D 320 THR cc_start: 0.9455 (m) cc_final: 0.9241 (p) REVERT: D 340 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7559 (tm-30) REVERT: F 571 TRP cc_start: 0.5623 (t60) cc_final: 0.5213 (t60) REVERT: F 634 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7315 (tm-30) outliers start: 51 outliers final: 43 residues processed: 211 average time/residue: 0.1192 time to fit residues: 38.3370 Evaluate side-chains 216 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 346 VAL 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 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 109 ILE 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 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 576 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 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 346 VAL Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 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: 5.9990 chunk 126 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN B 625 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 478 ASN F 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104238 restraints weight = 24309.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107261 restraints weight = 15734.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.109330 restraints weight = 11854.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110749 restraints weight = 9756.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111578 restraints weight = 8510.364| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15330 Z= 0.186 Angle : 0.682 7.417 21012 Z= 0.333 Chirality : 0.044 0.242 2649 Planarity : 0.004 0.055 2469 Dihedral : 5.269 49.344 1813 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.88 % Favored : 93.76 % Rotamer: Outliers : 3.36 % Allowed : 13.97 % Favored : 82.67 % 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: 1.03 (0.26), residues: 438 sheet: -0.37 (0.26), residues: 393 loop : -0.48 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 166 TYR 0.009 0.001 TYR D 217 PHE 0.025 0.002 PHE C 53 TRP 0.013 0.001 TRP F 623 HIS 0.002 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (15186) covalent geometry : angle 0.65350 / 0.33 (20616) SS BOND : bond 0.00478 / 0.29 ( 36) SS BOND : angle 1.16311 / 0.82 ( 72) hydrogen bonds : bond 0.04786 / 3.18 ( 573) hydrogen bonds : angle 4.73059 / 3.26 ( 1557) link_ALPHA1-2 : bond 0.00422 / 0.19 ( 3) link_ALPHA1-2 : angle 1.79842 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00630 / 0.28 ( 3) link_ALPHA1-3 : angle 1.08460 / 0.59 ( 9) link_ALPHA1-6 : bond 0.00314 / 0.14 ( 3) link_ALPHA1-6 : angle 1.39951 / 0.77 ( 9) link_BETA1-4 : bond 0.00370 / 0.24 ( 33) link_BETA1-4 : angle 1.24200 / 0.86 ( 99) link_BETA1-6 : bond 0.00343 / 0.19 ( 6) link_BETA1-6 : angle 1.07107 / 0.63 ( 18) link_NAG-ASN : bond 0.00339 / 0.22 ( 60) link_NAG-ASN : angle 1.88544 / 1.28 ( 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 225 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 209 SER cc_start: 0.8900 (t) cc_final: 0.8523 (p) REVERT: A 271 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7251 (mtp) REVERT: B 621 GLU cc_start: 0.8449 (tt0) cc_final: 0.7838 (tp30) REVERT: C 107 ASP cc_start: 0.8397 (m-30) cc_final: 0.8056 (t0) REVERT: C 125 LEU cc_start: 0.9304 (tp) cc_final: 0.8790 (tp) REVERT: C 207 LYS cc_start: 0.8663 (tppt) cc_final: 0.7884 (tmtt) REVERT: E 612 SER cc_start: 0.9067 (m) cc_final: 0.8729 (t) REVERT: E 616 ASN cc_start: 0.8729 (t0) cc_final: 0.8474 (t0) REVERT: D 125 LEU cc_start: 0.9228 (tp) cc_final: 0.8643 (tp) REVERT: D 209 SER cc_start: 0.8910 (t) cc_final: 0.8572 (p) REVERT: D 340 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7368 (tm-30) REVERT: F 634 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7341 (tm-30) outliers start: 51 outliers final: 46 residues processed: 208 average time/residue: 0.1185 time to fit residues: 37.5822 Evaluate side-chains 217 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 346 VAL 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 625 ASN Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 109 ILE 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 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 576 LEU Chi-restraints excluded: chain E residue 599 SER 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 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 346 VAL Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 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 82 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 422 GLN D 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104386 restraints weight = 24115.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107405 restraints weight = 15614.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109423 restraints weight = 11761.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110768 restraints weight = 9724.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111747 restraints weight = 8520.436| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 15330 Z= 0.266 Angle : 0.918 59.196 21012 Z= 0.530 Chirality : 0.044 0.332 2649 Planarity : 0.005 0.159 2469 Dihedral : 5.353 49.345 1813 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.88 % Favored : 93.71 % Rotamer: Outliers : 3.43 % Allowed : 14.10 % Favored : 82.48 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.05 (0.26), residues: 438 sheet: -0.37 (0.26), residues: 393 loop : -0.48 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 166 TYR 0.008 0.001 TYR A 484 PHE 0.024 0.002 PHE C 53 TRP 0.012 0.001 TRP F 623 HIS 0.003 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.27 (15186) covalent geometry : angle 0.90086 / 0.53 (20616) SS BOND : bond 0.00461 / 0.28 ( 36) SS BOND : angle 1.13711 / 0.81 ( 72) hydrogen bonds : bond 0.04782 / 3.18 ( 573) hydrogen bonds : angle 4.73032 / 3.26 ( 1557) link_ALPHA1-2 : bond 0.00424 / 0.19 ( 3) link_ALPHA1-2 : angle 1.79921 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00623 / 0.28 ( 3) link_ALPHA1-3 : angle 1.08203 / 0.59 ( 9) link_ALPHA1-6 : bond 0.00314 / 0.14 ( 3) link_ALPHA1-6 : angle 1.39992 / 0.77 ( 9) link_BETA1-4 : bond 0.00368 / 0.24 ( 33) link_BETA1-4 : angle 1.24394 / 0.87 ( 99) link_BETA1-6 : bond 0.00303 / 0.16 ( 6) link_BETA1-6 : angle 1.06212 / 0.62 ( 18) link_NAG-ASN : bond 0.00338 / 0.22 ( 60) link_NAG-ASN : angle 1.88518 / 1.27 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2136.82 seconds wall clock time: 38 minutes 1.12 seconds (2281.12 seconds total)