Starting phenix.real_space_refine on Sun Jun 22 15:39:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgu_41244/06_2025/8tgu_41244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgu_41244/06_2025/8tgu_41244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tgu_41244/06_2025/8tgu_41244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgu_41244/06_2025/8tgu_41244.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgu_41244/06_2025/8tgu_41244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgu_41244/06_2025/8tgu_41244.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13539 atoms to isotropic. 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 9258 2.51 5 N 2475 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4518 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 4 Chain: "B" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4518 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 4 Chain: "C" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4518 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 548} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 8.97, per 1000 atoms: 0.60 Number of scatterers: 14880 At special positions: 0 Unit cell: (132.84, 129.6, 129.6, 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 3039 8.00 N 2475 7.00 C 9258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.05 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 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 705 " - " ASN A 234 " " NAG A 706 " - " ASN A 339 " " NAG A 707 " - " ASN A 355 " " NAG A 708 " - " ASN A 386 " " NAG B 701 " - " ASN B 611 " " NAG B 704 " - " ASN B 262 " " NAG B 706 " - " ASN B 301 " " NAG B 707 " - " ASN B 355 " " NAG B 708 " - " ASN B 363 " " NAG C 704 " - " ASN C 133 " " NAG C 705 " - " ASN C 185 " " NAG C 706 " - " ASN C 339 " " NAG C 707 " - " ASN C 355 " " NAG C 708 " - " ASN C 363 " " NAG C 709 " - " ASN C 392 " " NAG D 1 " - " ASN A 88 " " NAG E 1 " - " ASN A 160 " " NAG F 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 301 " " NAG K 1 " - " ASN A 332 " " NAG L 1 " - " ASN A 363 " " NAG M 1 " - " ASN A 392 " " NAG N 1 " - " ASN A 448 " " NAG O 1 " - " ASN B 156 " " NAG P 1 " - " ASN B 160 " " NAG Q 1 " - " ASN B 197 " " NAG R 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 276 " " NAG V 1 " - " ASN B 332 " " NAG W 1 " - " ASN B 339 " " NAG X 1 " - " ASN B 392 " " NAG Y 1 " - " ASN B 448 " " NAG a 1 " - " ASN C 160 " " NAG b 1 " - " ASN C 197 " " NAG c 1 " - " ASN C 234 " " NAG e 1 " - " ASN C 276 " " NAG f 1 " - " ASN C 295 " " NAG g 1 " - " ASN C 301 " " NAG h 1 " - " ASN C 332 " " NAG i 1 " - " ASN C 386 " " NAG j 1 " - " ASN C 448 " Time building additional restraints: 5.08 Conformation dependent library (CDL) restraints added in 1.9 seconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 31 sheets defined 25.1% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.518A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.916A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.547A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.701A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.036A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 4.082A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.530A pdb=" N SER A 615 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.584A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.889A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 662 Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.704A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 350 removed outlier: 3.735A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.625A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 4.098A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.287A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.544A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.796A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 662 Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.224A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.308A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.225A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.638A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 544 removed outlier: 4.242A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 596 removed outlier: 4.418A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 633 Processing helix chain 'C' and resid 638 through 649 Processing helix chain 'C' and resid 650 through 663 removed outlier: 4.686A pdb=" N LEU C 660 " --> pdb=" O ASN C 656 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 663 " --> pdb=" O ASP C 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.274A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N CYS A 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: 3.624A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.123A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.766A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.632A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.006A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.216A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.702A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 76 removed outlier: 7.130A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.740A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'B' and resid 158 through 162 Processing sheet with id=AB9, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.700A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.688A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.648A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 419 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AC4, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.818A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.509A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.831A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 169 through 177 removed outlier: 4.693A pdb=" N GLU C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.856A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.517A pdb=" N VAL C 286 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 452 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AD3, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.555A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 419 " --> pdb=" O TYR C 384 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 423 through 424 455 hydrogen bonds defined for protein. 1260 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: 5.02 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4660 1.35 - 1.47: 3859 1.47 - 1.60: 6490 1.60 - 1.73: 0 1.73 - 1.85: 144 Bond restraints: 15153 Sorted by residual: bond pdb=" N GLY C 521 " pdb=" CA GLY C 521 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.43e+00 bond pdb=" N GLY B 521 " pdb=" CA GLY B 521 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.92e+00 bond pdb=" N GLY A 521 " pdb=" CA GLY A 521 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.90e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C1 NAG Y 1 " pdb=" C2 NAG Y 1 " ideal model delta sigma weight residual 1.532 1.490 0.042 2.00e-02 2.50e+03 4.48e+00 ... (remaining 15148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 20314 2.96 - 5.92: 228 5.92 - 8.88: 24 8.88 - 11.83: 1 11.83 - 14.79: 1 Bond angle restraints: 20568 Sorted by residual: angle pdb=" C SER C 460 " pdb=" N THR C 461 " pdb=" CA THR C 461 " ideal model delta sigma weight residual 121.70 136.49 -14.79 1.80e+00 3.09e-01 6.75e+01 angle pdb=" N ILE C 622 " pdb=" CA ILE C 622 " pdb=" C ILE C 622 " ideal model delta sigma weight residual 111.45 107.95 3.50 9.30e-01 1.16e+00 1.42e+01 angle pdb=" CB GLU B 584 " pdb=" CG GLU B 584 " pdb=" CD GLU B 584 " ideal model delta sigma weight residual 112.60 118.43 -5.83 1.70e+00 3.46e-01 1.18e+01 angle pdb=" CB MET C 475 " pdb=" CG MET C 475 " pdb=" SD MET C 475 " ideal model delta sigma weight residual 112.70 122.97 -10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA CYS B 418 " pdb=" CB CYS B 418 " pdb=" SG CYS B 418 " ideal model delta sigma weight residual 114.40 122.03 -7.63 2.30e+00 1.89e-01 1.10e+01 ... (remaining 20563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.26: 9745 25.26 - 50.52: 479 50.52 - 75.78: 75 75.78 - 101.04: 52 101.04 - 126.31: 38 Dihedral angle restraints: 10389 sinusoidal: 5424 harmonic: 4965 Sorted by residual: dihedral pdb=" CA ASN A 462 " pdb=" C ASN A 462 " pdb=" N SER A 463 " pdb=" CA SER A 463 " ideal model delta harmonic sigma weight residual 180.00 -145.69 -34.31 0 5.00e+00 4.00e-02 4.71e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -143.24 57.24 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 41.18 51.82 1 1.00e+01 1.00e-02 3.67e+01 ... (remaining 10386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 2567 0.192 - 0.383: 13 0.383 - 0.574: 1 0.574 - 0.766: 0 0.766 - 0.957: 1 Chirality restraints: 2582 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN B 448 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-01 2.50e+01 2.29e+01 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B 392 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2579 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 84 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ILE A 84 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE A 84 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS A 85 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 584 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" CD GLU A 584 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU A 584 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 584 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 392 " 0.020 2.00e-02 2.50e+03 1.85e-02 4.29e+00 pdb=" CG ASN B 392 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 392 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 392 " -0.022 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 445 2.71 - 3.26: 14377 3.26 - 3.80: 21141 3.80 - 4.35: 26783 4.35 - 4.90: 46139 Nonbonded interactions: 108885 Sorted by model distance: nonbonded pdb=" OE1 GLN A 258 " pdb=" OG1 THR A 387 " model vdw 2.159 3.040 nonbonded pdb=" O3 NAG C 701 " pdb=" O6 NAG C 701 " model vdw 2.186 3.040 nonbonded pdb=" OD1 ASN C 136 " pdb=" ND2 ASN C 156 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLU B 211 " pdb=" O4 NAG B 705 " model vdw 2.219 3.040 nonbonded pdb=" O ILE A 595 " pdb=" ND2 ASN A 651 " model vdw 2.255 3.120 ... (remaining 108880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 34 through 664 or resid 701 through 708)) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' 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 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.190 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 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 : 0.006 0.051 15269 Z= 0.261 Angle : 0.902 14.792 20883 Z= 0.414 Chirality : 0.056 0.957 2582 Planarity : 0.004 0.058 2502 Dihedral : 17.148 126.305 7074 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1689 helix: 0.52 (0.28), residues: 397 sheet: -1.04 (0.25), residues: 411 loop : -1.42 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 631 HIS 0.006 0.001 HIS B 374 PHE 0.010 0.001 PHE A 353 TYR 0.025 0.002 TYR C 191 ARG 0.012 0.001 ARG B 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 45) link_NAG-ASN : angle 2.86202 ( 135) link_BETA1-4 : bond 0.00689 ( 38) link_BETA1-4 : angle 3.54400 ( 114) hydrogen bonds : bond 0.21327 ( 455) hydrogen bonds : angle 8.15595 ( 1260) SS BOND : bond 0.00560 ( 33) SS BOND : angle 1.68757 ( 66) covalent geometry : bond 0.00558 (15153) covalent geometry : angle 0.83250 (20568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8807 (tpt) cc_final: 0.7773 (tpt) REVERT: A 269 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6635 (tt0) REVERT: A 427 TRP cc_start: 0.6926 (m-10) cc_final: 0.6683 (m-90) REVERT: A 607 ASN cc_start: 0.7349 (t0) cc_final: 0.7080 (t0) REVERT: A 632 ASP cc_start: 0.8177 (t70) cc_final: 0.7794 (t0) REVERT: B 271 MET cc_start: 0.7366 (mmm) cc_final: 0.7141 (tpt) REVERT: B 308 ARG cc_start: 0.8581 (ptp-110) cc_final: 0.8379 (ptp-110) REVERT: B 584 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7377 (mt-10) REVERT: B 614 TRP cc_start: 0.7696 (m-10) cc_final: 0.7391 (m-90) REVERT: C 502 LYS cc_start: 0.7348 (tttm) cc_final: 0.6534 (mttt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2944 time to fit residues: 76.9796 Evaluate side-chains 151 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.143131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.123482 restraints weight = 19088.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.124458 restraints weight = 23326.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125376 restraints weight = 22204.365| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15269 Z= 0.136 Angle : 0.721 15.713 20883 Z= 0.334 Chirality : 0.049 0.493 2582 Planarity : 0.004 0.040 2502 Dihedral : 12.492 99.015 3834 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 0.92 % Allowed : 5.05 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1689 helix: 0.95 (0.29), residues: 402 sheet: -0.79 (0.25), residues: 405 loop : -1.43 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 631 HIS 0.005 0.001 HIS B 374 PHE 0.023 0.002 PHE C 53 TYR 0.010 0.001 TYR B 484 ARG 0.005 0.000 ARG A 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 45) link_NAG-ASN : angle 3.06331 ( 135) link_BETA1-4 : bond 0.00520 ( 38) link_BETA1-4 : angle 2.04985 ( 114) hydrogen bonds : bond 0.04493 ( 455) hydrogen bonds : angle 5.79074 ( 1260) SS BOND : bond 0.00419 ( 33) SS BOND : angle 1.23284 ( 66) covalent geometry : bond 0.00310 (15153) covalent geometry : angle 0.66174 (20568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6588 (p-90) cc_final: 0.5184 (p-90) REVERT: A 161 MET cc_start: 0.8272 (tpt) cc_final: 0.7516 (tpt) REVERT: A 427 TRP cc_start: 0.7605 (m-10) cc_final: 0.7378 (m-90) REVERT: A 542 ARG cc_start: 0.8205 (ttp-110) cc_final: 0.7914 (ttm110) REVERT: A 581 LEU cc_start: 0.9115 (tt) cc_final: 0.8875 (tp) REVERT: A 607 ASN cc_start: 0.7544 (t0) cc_final: 0.7259 (t0) REVERT: B 69 TRP cc_start: 0.6526 (p-90) cc_final: 0.5583 (p-90) REVERT: B 104 MET cc_start: 0.8546 (tpp) cc_final: 0.7926 (ttt) REVERT: B 271 MET cc_start: 0.7723 (mmm) cc_final: 0.7433 (tpt) REVERT: B 308 ARG cc_start: 0.8090 (ptp-110) cc_final: 0.7869 (ptp-110) REVERT: B 387 THR cc_start: 0.8913 (p) cc_final: 0.7967 (m) REVERT: B 502 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7347 (tmtt) REVERT: B 647 GLU cc_start: 0.8371 (pt0) cc_final: 0.7820 (pt0) REVERT: C 125 LEU cc_start: 0.9222 (tp) cc_final: 0.8926 (tp) REVERT: C 502 LYS cc_start: 0.7573 (tttm) cc_final: 0.7308 (mttt) REVERT: C 621 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6854 (mt-10) outliers start: 14 outliers final: 8 residues processed: 170 average time/residue: 0.2966 time to fit residues: 73.9998 Evaluate side-chains 150 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain C residue 184 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 110 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 161 optimal weight: 0.0870 chunk 119 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.144266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.124461 restraints weight = 19084.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.123701 restraints weight = 20617.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123887 restraints weight = 21557.946| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15269 Z= 0.113 Angle : 0.646 12.114 20883 Z= 0.301 Chirality : 0.048 0.506 2582 Planarity : 0.003 0.053 2502 Dihedral : 8.508 57.336 3834 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 1.51 % Allowed : 7.48 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1689 helix: 1.14 (0.28), residues: 402 sheet: -0.54 (0.26), residues: 402 loop : -1.38 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 631 HIS 0.005 0.001 HIS B 374 PHE 0.022 0.001 PHE C 53 TYR 0.007 0.001 TYR A 191 ARG 0.004 0.000 ARG C 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 45) link_NAG-ASN : angle 2.66699 ( 135) link_BETA1-4 : bond 0.00476 ( 38) link_BETA1-4 : angle 1.94636 ( 114) hydrogen bonds : bond 0.03646 ( 455) hydrogen bonds : angle 5.14229 ( 1260) SS BOND : bond 0.00458 ( 33) SS BOND : angle 1.33087 ( 66) covalent geometry : bond 0.00254 (15153) covalent geometry : angle 0.59229 (20568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8280 (tpt) cc_final: 0.7597 (tpt) REVERT: A 542 ARG cc_start: 0.8221 (ttp-110) cc_final: 0.7888 (ttm110) REVERT: A 607 ASN cc_start: 0.7878 (t0) cc_final: 0.7502 (t0) REVERT: B 104 MET cc_start: 0.8463 (tpp) cc_final: 0.8166 (ttt) REVERT: B 180 ASP cc_start: 0.8149 (t0) cc_final: 0.7353 (t0) REVERT: B 271 MET cc_start: 0.7620 (mmm) cc_final: 0.7330 (tpt) REVERT: B 308 ARG cc_start: 0.8043 (ptp-110) cc_final: 0.7824 (ptp-110) REVERT: B 387 THR cc_start: 0.8800 (p) cc_final: 0.7799 (m) REVERT: B 647 GLU cc_start: 0.8354 (pt0) cc_final: 0.7861 (pt0) REVERT: C 125 LEU cc_start: 0.9193 (tp) cc_final: 0.8762 (tp) outliers start: 23 outliers final: 13 residues processed: 174 average time/residue: 0.2878 time to fit residues: 73.5893 Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 595 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 0.0020 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.143172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123792 restraints weight = 19044.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.122848 restraints weight = 20801.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.122837 restraints weight = 21785.701| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15269 Z= 0.118 Angle : 0.617 10.618 20883 Z= 0.293 Chirality : 0.046 0.506 2582 Planarity : 0.004 0.055 2502 Dihedral : 7.374 58.246 3834 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 1.97 % Allowed : 8.66 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.21), residues: 1689 helix: 1.23 (0.29), residues: 401 sheet: -0.55 (0.25), residues: 404 loop : -1.33 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 631 HIS 0.006 0.001 HIS B 374 PHE 0.021 0.001 PHE C 53 TYR 0.011 0.001 TYR B 484 ARG 0.006 0.000 ARG B 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 45) link_NAG-ASN : angle 2.55777 ( 135) link_BETA1-4 : bond 0.00422 ( 38) link_BETA1-4 : angle 1.77142 ( 114) hydrogen bonds : bond 0.03460 ( 455) hydrogen bonds : angle 4.88319 ( 1260) SS BOND : bond 0.00405 ( 33) SS BOND : angle 1.26617 ( 66) covalent geometry : bond 0.00273 (15153) covalent geometry : angle 0.56654 (20568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.629 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8316 (tpt) cc_final: 0.7521 (ttt) REVERT: A 542 ARG cc_start: 0.8300 (ttp-110) cc_final: 0.8036 (ttm110) REVERT: A 607 ASN cc_start: 0.7890 (t0) cc_final: 0.7554 (t0) REVERT: B 104 MET cc_start: 0.8486 (tpp) cc_final: 0.8269 (ttt) REVERT: B 180 ASP cc_start: 0.8171 (t0) cc_final: 0.7295 (t0) REVERT: B 271 MET cc_start: 0.7614 (mmm) cc_final: 0.7315 (tpt) REVERT: B 308 ARG cc_start: 0.8065 (ptp-110) cc_final: 0.7844 (ptp-110) REVERT: B 387 THR cc_start: 0.8819 (p) cc_final: 0.8574 (t) REVERT: B 647 GLU cc_start: 0.8374 (pt0) cc_final: 0.7885 (pt0) REVERT: C 125 LEU cc_start: 0.9212 (tp) cc_final: 0.8805 (tp) REVERT: C 161 MET cc_start: 0.7624 (ttm) cc_final: 0.7390 (ttm) REVERT: C 625 ASN cc_start: 0.7428 (t0) cc_final: 0.6958 (t0) outliers start: 30 outliers final: 14 residues processed: 177 average time/residue: 0.2658 time to fit residues: 70.8161 Evaluate side-chains 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 647 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 138 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.143133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123919 restraints weight = 19125.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123927 restraints weight = 25910.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.124334 restraints weight = 23946.469| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15269 Z= 0.118 Angle : 0.616 10.292 20883 Z= 0.294 Chirality : 0.046 0.498 2582 Planarity : 0.003 0.059 2502 Dihedral : 7.057 58.243 3834 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.44 % Favored : 95.44 % Rotamer: Outliers : 1.38 % Allowed : 10.17 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1689 helix: 1.28 (0.29), residues: 399 sheet: -0.55 (0.25), residues: 399 loop : -1.28 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 631 HIS 0.005 0.001 HIS B 374 PHE 0.018 0.001 PHE C 53 TYR 0.019 0.001 TYR C 486 ARG 0.006 0.000 ARG B 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 45) link_NAG-ASN : angle 2.50461 ( 135) link_BETA1-4 : bond 0.00420 ( 38) link_BETA1-4 : angle 1.66390 ( 114) hydrogen bonds : bond 0.03365 ( 455) hydrogen bonds : angle 4.76561 ( 1260) SS BOND : bond 0.00408 ( 33) SS BOND : angle 1.54851 ( 66) covalent geometry : bond 0.00275 (15153) covalent geometry : angle 0.56684 (20568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8366 (tpt) cc_final: 0.7548 (ttt) REVERT: A 542 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7986 (ttm110) REVERT: B 91 GLU cc_start: 0.8097 (tp30) cc_final: 0.7733 (tp30) REVERT: B 104 MET cc_start: 0.8507 (tpp) cc_final: 0.8287 (ttt) REVERT: B 180 ASP cc_start: 0.8200 (t0) cc_final: 0.7334 (t0) REVERT: B 246 GLN cc_start: 0.8637 (tp40) cc_final: 0.8433 (tp40) REVERT: B 387 THR cc_start: 0.8837 (p) cc_final: 0.8608 (t) REVERT: B 530 MET cc_start: 0.6446 (ttp) cc_final: 0.5879 (ttp) REVERT: B 603 ILE cc_start: 0.7301 (mt) cc_final: 0.6968 (mt) REVERT: B 647 GLU cc_start: 0.8385 (pt0) cc_final: 0.7816 (pt0) REVERT: C 125 LEU cc_start: 0.9213 (tp) cc_final: 0.8773 (tp) REVERT: C 161 MET cc_start: 0.7609 (ttm) cc_final: 0.7321 (ttm) REVERT: C 502 LYS cc_start: 0.7657 (tttm) cc_final: 0.7443 (mttm) REVERT: C 659 ASP cc_start: 0.5263 (m-30) cc_final: 0.4664 (m-30) outliers start: 21 outliers final: 15 residues processed: 167 average time/residue: 0.2619 time to fit residues: 65.4523 Evaluate side-chains 156 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 108 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.141375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.121903 restraints weight = 19142.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.121301 restraints weight = 21011.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121386 restraints weight = 21482.465| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15269 Z= 0.138 Angle : 0.625 10.242 20883 Z= 0.299 Chirality : 0.046 0.502 2582 Planarity : 0.004 0.061 2502 Dihedral : 6.859 59.696 3834 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 1.51 % Allowed : 11.09 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1689 helix: 1.29 (0.29), residues: 399 sheet: -0.51 (0.25), residues: 406 loop : -1.31 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 631 HIS 0.006 0.001 HIS B 374 PHE 0.019 0.002 PHE C 53 TYR 0.014 0.001 TYR C 486 ARG 0.006 0.000 ARG B 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 45) link_NAG-ASN : angle 2.60061 ( 135) link_BETA1-4 : bond 0.00411 ( 38) link_BETA1-4 : angle 1.61424 ( 114) hydrogen bonds : bond 0.03584 ( 455) hydrogen bonds : angle 4.76795 ( 1260) SS BOND : bond 0.00432 ( 33) SS BOND : angle 1.40750 ( 66) covalent geometry : bond 0.00330 (15153) covalent geometry : angle 0.57594 (20568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.690 Fit side-chains REVERT: A 161 MET cc_start: 0.8385 (tpt) cc_final: 0.7571 (ttt) REVERT: A 542 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.8012 (ttm110) REVERT: B 69 TRP cc_start: 0.6731 (p-90) cc_final: 0.5893 (p-90) REVERT: B 104 MET cc_start: 0.8514 (tpp) cc_final: 0.8264 (ttt) REVERT: B 180 ASP cc_start: 0.8268 (t0) cc_final: 0.7427 (t0) REVERT: B 530 MET cc_start: 0.6408 (ttp) cc_final: 0.5860 (ttp) REVERT: B 647 GLU cc_start: 0.8371 (pt0) cc_final: 0.7766 (pt0) REVERT: B 655 LYS cc_start: 0.7625 (tptt) cc_final: 0.7179 (tptt) REVERT: B 658 GLN cc_start: 0.8202 (tt0) cc_final: 0.7884 (tt0) REVERT: C 125 LEU cc_start: 0.9263 (tp) cc_final: 0.8798 (tp) REVERT: C 161 MET cc_start: 0.7583 (ttm) cc_final: 0.7338 (ttm) REVERT: C 271 MET cc_start: 0.8016 (mmm) cc_final: 0.7348 (mmt) REVERT: C 502 LYS cc_start: 0.7688 (tttm) cc_final: 0.7468 (mttm) REVERT: C 530 MET cc_start: 0.8977 (mtm) cc_final: 0.8604 (mtp) outliers start: 23 outliers final: 16 residues processed: 158 average time/residue: 0.2711 time to fit residues: 64.6579 Evaluate side-chains 151 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 139 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.141048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.121011 restraints weight = 18934.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.120468 restraints weight = 19736.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.120533 restraints weight = 19854.815| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15269 Z= 0.146 Angle : 0.631 10.113 20883 Z= 0.302 Chirality : 0.047 0.513 2582 Planarity : 0.004 0.061 2502 Dihedral : 6.763 59.905 3834 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.03 % Rotamer: Outliers : 1.51 % Allowed : 11.81 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.21), residues: 1689 helix: 1.29 (0.29), residues: 399 sheet: -0.57 (0.26), residues: 376 loop : -1.32 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 631 HIS 0.006 0.001 HIS B 374 PHE 0.018 0.002 PHE C 53 TYR 0.012 0.001 TYR C 486 ARG 0.008 0.000 ARG B 504 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 45) link_NAG-ASN : angle 2.58524 ( 135) link_BETA1-4 : bond 0.00408 ( 38) link_BETA1-4 : angle 1.58544 ( 114) hydrogen bonds : bond 0.03644 ( 455) hydrogen bonds : angle 4.76941 ( 1260) SS BOND : bond 0.00491 ( 33) SS BOND : angle 1.37536 ( 66) covalent geometry : bond 0.00350 (15153) covalent geometry : angle 0.58312 (20568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.526 Fit side-chains REVERT: A 161 MET cc_start: 0.8391 (tpt) cc_final: 0.7567 (ttt) REVERT: B 69 TRP cc_start: 0.6766 (p-90) cc_final: 0.5850 (p-90) REVERT: B 104 MET cc_start: 0.8556 (tpp) cc_final: 0.8278 (ttt) REVERT: B 180 ASP cc_start: 0.8326 (t0) cc_final: 0.7425 (t0) REVERT: B 289 ASN cc_start: 0.8733 (p0) cc_final: 0.8393 (p0) REVERT: B 530 MET cc_start: 0.6522 (ttp) cc_final: 0.6014 (ttp) REVERT: B 647 GLU cc_start: 0.8378 (pt0) cc_final: 0.8035 (pt0) REVERT: C 125 LEU cc_start: 0.9283 (tp) cc_final: 0.8782 (tp) REVERT: C 271 MET cc_start: 0.8026 (mmm) cc_final: 0.7340 (mmt) REVERT: C 530 MET cc_start: 0.9001 (mtm) cc_final: 0.8591 (mtp) REVERT: C 625 ASN cc_start: 0.7253 (t0) cc_final: 0.6865 (t0) outliers start: 23 outliers final: 16 residues processed: 159 average time/residue: 0.2566 time to fit residues: 61.5889 Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.140914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.122303 restraints weight = 18841.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.121247 restraints weight = 22922.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.121643 restraints weight = 24364.954| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15269 Z= 0.142 Angle : 0.639 10.194 20883 Z= 0.307 Chirality : 0.047 0.509 2582 Planarity : 0.004 0.062 2502 Dihedral : 6.754 59.752 3834 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.15 % Rotamer: Outliers : 1.64 % Allowed : 12.20 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.21), residues: 1689 helix: 1.30 (0.29), residues: 399 sheet: -0.55 (0.26), residues: 376 loop : -1.34 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 631 HIS 0.006 0.001 HIS B 374 PHE 0.017 0.002 PHE C 53 TYR 0.011 0.001 TYR C 486 ARG 0.007 0.000 ARG C 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 45) link_NAG-ASN : angle 2.57677 ( 135) link_BETA1-4 : bond 0.00401 ( 38) link_BETA1-4 : angle 1.56988 ( 114) hydrogen bonds : bond 0.03606 ( 455) hydrogen bonds : angle 4.74252 ( 1260) SS BOND : bond 0.00478 ( 33) SS BOND : angle 1.56736 ( 66) covalent geometry : bond 0.00341 (15153) covalent geometry : angle 0.59065 (20568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.551 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8401 (tpt) cc_final: 0.7563 (ttt) REVERT: A 540 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: A 542 ARG cc_start: 0.8438 (ttm110) cc_final: 0.8201 (ttm110) REVERT: B 69 TRP cc_start: 0.6783 (p-90) cc_final: 0.5834 (p-90) REVERT: B 104 MET cc_start: 0.8587 (tpp) cc_final: 0.8288 (ttt) REVERT: B 180 ASP cc_start: 0.8366 (t0) cc_final: 0.7472 (t0) REVERT: B 289 ASN cc_start: 0.8796 (p0) cc_final: 0.8440 (p0) REVERT: B 530 MET cc_start: 0.6521 (ttp) cc_final: 0.5997 (ttp) REVERT: B 647 GLU cc_start: 0.8164 (pt0) cc_final: 0.7815 (pt0) REVERT: B 655 LYS cc_start: 0.7551 (tptt) cc_final: 0.7107 (tptt) REVERT: B 664 ASP cc_start: 0.7263 (p0) cc_final: 0.7004 (p0) REVERT: C 125 LEU cc_start: 0.9224 (tp) cc_final: 0.8776 (tp) REVERT: C 271 MET cc_start: 0.7988 (mmm) cc_final: 0.7315 (mmt) REVERT: C 502 LYS cc_start: 0.7589 (mttm) cc_final: 0.7370 (mmmm) REVERT: C 530 MET cc_start: 0.9008 (mtm) cc_final: 0.8703 (mtp) REVERT: C 625 ASN cc_start: 0.7212 (t0) cc_final: 0.6861 (t0) outliers start: 25 outliers final: 18 residues processed: 158 average time/residue: 0.2739 time to fit residues: 65.1135 Evaluate side-chains 155 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 652 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 128 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN C 85 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.145942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.122635 restraints weight = 18945.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.123784 restraints weight = 16425.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.124933 restraints weight = 14810.205| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15269 Z= 0.141 Angle : 0.632 10.120 20883 Z= 0.304 Chirality : 0.047 0.504 2582 Planarity : 0.004 0.059 2502 Dihedral : 6.664 59.564 3834 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 1.51 % Allowed : 12.40 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1689 helix: 1.32 (0.29), residues: 399 sheet: -0.50 (0.25), residues: 400 loop : -1.33 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.006 0.001 HIS B 374 PHE 0.018 0.002 PHE C 159 TYR 0.011 0.001 TYR C 486 ARG 0.004 0.000 ARG B 419 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 45) link_NAG-ASN : angle 2.52811 ( 135) link_BETA1-4 : bond 0.00398 ( 38) link_BETA1-4 : angle 1.54412 ( 114) hydrogen bonds : bond 0.03572 ( 455) hydrogen bonds : angle 4.71970 ( 1260) SS BOND : bond 0.00522 ( 33) SS BOND : angle 1.68259 ( 66) covalent geometry : bond 0.00338 (15153) covalent geometry : angle 0.58427 (20568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.492 Fit side-chains REVERT: A 161 MET cc_start: 0.8407 (tpt) cc_final: 0.7591 (ttt) REVERT: A 540 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: A 542 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8262 (ttm110) REVERT: B 69 TRP cc_start: 0.6682 (p-90) cc_final: 0.5743 (p-90) REVERT: B 104 MET cc_start: 0.8569 (tpp) cc_final: 0.8303 (ttt) REVERT: B 180 ASP cc_start: 0.8404 (t0) cc_final: 0.7467 (t0) REVERT: B 289 ASN cc_start: 0.8870 (p0) cc_final: 0.8492 (p0) REVERT: B 530 MET cc_start: 0.6510 (ttp) cc_final: 0.6022 (ttp) REVERT: B 647 GLU cc_start: 0.8075 (pt0) cc_final: 0.7733 (pt0) REVERT: B 655 LYS cc_start: 0.7494 (tptt) cc_final: 0.7071 (tptt) REVERT: B 664 ASP cc_start: 0.7404 (p0) cc_final: 0.7149 (p0) REVERT: C 125 LEU cc_start: 0.9192 (tp) cc_final: 0.8740 (tp) REVERT: C 271 MET cc_start: 0.8081 (mmm) cc_final: 0.7419 (mmt) REVERT: C 502 LYS cc_start: 0.7671 (mttm) cc_final: 0.7346 (mmmm) REVERT: C 530 MET cc_start: 0.9067 (mtm) cc_final: 0.8746 (mtp) REVERT: C 625 ASN cc_start: 0.7307 (t0) cc_final: 0.7021 (t0) outliers start: 23 outliers final: 17 residues processed: 156 average time/residue: 0.2565 time to fit residues: 60.1398 Evaluate side-chains 156 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 652 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 71 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 118 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.145384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.121949 restraints weight = 19068.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123200 restraints weight = 16299.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.124323 restraints weight = 14690.893| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15269 Z= 0.122 Angle : 0.620 10.084 20883 Z= 0.298 Chirality : 0.046 0.496 2582 Planarity : 0.003 0.059 2502 Dihedral : 6.541 58.689 3834 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 1.18 % Allowed : 12.93 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1689 helix: 1.33 (0.29), residues: 399 sheet: -0.53 (0.26), residues: 383 loop : -1.30 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 571 HIS 0.005 0.001 HIS B 374 PHE 0.016 0.001 PHE C 53 TYR 0.015 0.001 TYR C 486 ARG 0.003 0.000 ARG B 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 45) link_NAG-ASN : angle 2.51023 ( 135) link_BETA1-4 : bond 0.00397 ( 38) link_BETA1-4 : angle 1.51845 ( 114) hydrogen bonds : bond 0.03382 ( 455) hydrogen bonds : angle 4.64688 ( 1260) SS BOND : bond 0.00473 ( 33) SS BOND : angle 1.62772 ( 66) covalent geometry : bond 0.00288 (15153) covalent geometry : angle 0.57288 (20568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8388 (tpt) cc_final: 0.7588 (ttt) REVERT: A 540 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: A 542 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8289 (ttm110) REVERT: B 69 TRP cc_start: 0.6662 (p-90) cc_final: 0.5757 (p-90) REVERT: B 104 MET cc_start: 0.8530 (tpp) cc_final: 0.8291 (ttt) REVERT: B 180 ASP cc_start: 0.8384 (t0) cc_final: 0.7455 (t0) REVERT: B 289 ASN cc_start: 0.8864 (p0) cc_final: 0.8493 (p0) REVERT: B 530 MET cc_start: 0.6553 (ttp) cc_final: 0.6087 (ttp) REVERT: B 647 GLU cc_start: 0.8044 (pt0) cc_final: 0.7705 (pt0) REVERT: B 655 LYS cc_start: 0.7586 (tptt) cc_final: 0.7055 (tptt) REVERT: C 125 LEU cc_start: 0.9167 (tp) cc_final: 0.8721 (tp) REVERT: C 271 MET cc_start: 0.8078 (mmm) cc_final: 0.7416 (mmt) REVERT: C 530 MET cc_start: 0.9052 (mtm) cc_final: 0.8777 (mtp) REVERT: C 625 ASN cc_start: 0.7320 (t0) cc_final: 0.7041 (t0) outliers start: 18 outliers final: 17 residues processed: 153 average time/residue: 0.2886 time to fit residues: 67.2094 Evaluate side-chains 156 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 652 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 2.9990 chunk 161 optimal weight: 0.0040 chunk 162 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.0050 chunk 129 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.147949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.124351 restraints weight = 18967.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.125544 restraints weight = 18952.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.126776 restraints weight = 17062.476| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15269 Z= 0.104 Angle : 0.599 10.977 20883 Z= 0.286 Chirality : 0.045 0.478 2582 Planarity : 0.003 0.056 2502 Dihedral : 6.293 59.285 3834 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 1.05 % Allowed : 12.93 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1689 helix: 1.43 (0.29), residues: 399 sheet: -0.40 (0.25), residues: 411 loop : -1.27 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.003 0.001 HIS B 374 PHE 0.015 0.001 PHE C 53 TYR 0.013 0.001 TYR C 486 ARG 0.003 0.000 ARG B 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 45) link_NAG-ASN : angle 2.36414 ( 135) link_BETA1-4 : bond 0.00401 ( 38) link_BETA1-4 : angle 1.47600 ( 114) hydrogen bonds : bond 0.03070 ( 455) hydrogen bonds : angle 4.52330 ( 1260) SS BOND : bond 0.00422 ( 33) SS BOND : angle 1.38067 ( 66) covalent geometry : bond 0.00238 (15153) covalent geometry : angle 0.55660 (20568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4208.92 seconds wall clock time: 74 minutes 10.12 seconds (4450.12 seconds total)