Starting phenix.real_space_refine on Sat Sep 12 09:01:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vfl_21186/09_2026/6vfl_21186.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vfl_21186/09_2026/6vfl_21186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vfl_21186/09_2026/6vfl_21186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vfl_21186/09_2026/6vfl_21186.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vfl_21186/09_2026/6vfl_21186.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vfl_21186/09_2026/6vfl_21186.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vfl_21186/09_2026/6vfl_21186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vfl_21186/09_2026/6vfl_21186.map" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9306 2.51 5 N 2466 2.21 5 O 3054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14925 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 chiralities: 8 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 chiralities: 8 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 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 chiralities: 8 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.80, per 1000 atoms: 0.25 Number of scatterers: 14925 At special positions: 0 Unit cell: (129.95, 125.35, 115, 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 99 16.00 O 3054 8.00 N 2466 7.00 C 9306 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 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.11 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.11 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.11 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA Q 3 " - " MAN Q 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG 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 608 " - " ASN A 160 " " NAG A 609 " - " ASN A 276 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 363 " " NAG A 618 " - " ASN A 133 " " NAG A 627 " - " ASN A 289 " " NAG A 630 " - " ASN A 339 " " NAG A 631 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 608 " - " ASN C 160 " " NAG C 609 " - " ASN C 276 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 363 " " NAG C 618 " - " ASN C 133 " " NAG C 627 " - " ASN C 289 " " NAG C 630 " - " ASN C 339 " " NAG C 631 " - " ASN C 355 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 276 " " NAG E 612 " - " ASN E 386 " " NAG E 613 " - " ASN E 363 " " NAG E 618 " - " ASN E 133 " " NAG E 627 " - " ASN E 289 " " NAG E 630 " - " ASN E 339 " " NAG E 631 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 197 " " NAG L 1 " - " ASN A 156 " " NAG M 1 " - " ASN A 301 " " NAG N 1 " - " ASN A 88 " " NAG O 1 " - " ASN A 241 " " NAG P 1 " - " ASN A 332 " " NAG Q 1 " - " ASN C 262 " " NAG R 1 " - " ASN C 448 " " NAG S 1 " - " ASN C 295 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 197 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 241 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN E 262 " " NAG b 1 " - " ASN E 448 " " NAG c 1 " - " ASN E 295 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 301 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 241 " " NAG j 1 " - " ASN E 332 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 632.2 milliseconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 33 sheets defined 29.3% alpha, 51.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.228A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.930A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.113A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.919A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.830A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 544 No H-bonds generated for 'chain 'B' and resid 543 through 544' Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.543A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.228A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.928A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.113A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.919A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.831A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 544 No H-bonds generated for 'chain 'D' and resid 543 through 544' Processing helix chain 'D' and resid 545 through 549 Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.542A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 658 Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.227A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.928A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.113A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.919A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.830A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 544 No H-bonds generated for 'chain 'F' and resid 543 through 544' Processing helix chain 'F' and resid 545 through 549 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.543A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.601A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.706A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.515A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 4.080A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 316 through 323A removed outlier: 5.409A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.124A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.512A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.602A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.706A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.516A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 274 removed outlier: 4.081A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 316 through 323A removed outlier: 5.409A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.124A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.512A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.601A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.705A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.515A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.825A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 274 removed outlier: 4.082A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.408A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.124A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 10.825A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.772A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.815A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 393 through 395 removed outlier: 6.512A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3408 1.32 - 1.45: 4543 1.45 - 1.58: 7118 1.58 - 1.72: 3 1.72 - 1.85: 129 Bond restraints: 15201 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.416 0.081 1.40e-02 5.10e+03 3.33e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.29e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" NE1 TRP C 479 " pdb=" CE2 TRP C 479 " ideal model delta sigma weight residual 1.370 1.320 0.050 1.10e-02 8.26e+03 2.05e+01 bond pdb=" NE1 TRP A 479 " pdb=" CE2 TRP A 479 " ideal model delta sigma weight residual 1.370 1.321 0.049 1.10e-02 8.26e+03 2.02e+01 ... (remaining 15196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 15903 1.78 - 3.56: 3692 3.56 - 5.34: 814 5.34 - 7.12: 192 7.12 - 8.90: 36 Bond angle restraints: 20637 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 128.46 -8.90 1.01e+00 9.80e-01 7.77e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 128.46 -8.90 1.01e+00 9.80e-01 7.76e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 128.42 -8.86 1.01e+00 9.80e-01 7.70e+01 angle pdb=" N GLN A 258 " pdb=" CA GLN A 258 " pdb=" C GLN A 258 " ideal model delta sigma weight residual 111.36 118.69 -7.33 1.09e+00 8.42e-01 4.52e+01 angle pdb=" N GLN C 258 " pdb=" CA GLN C 258 " pdb=" C GLN C 258 " ideal model delta sigma weight residual 111.36 118.68 -7.32 1.09e+00 8.42e-01 4.51e+01 ... (remaining 20632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 7965 16.37 - 32.75: 234 32.75 - 49.12: 84 49.12 - 65.49: 21 65.49 - 81.87: 18 Dihedral angle restraints: 8322 sinusoidal: 3384 harmonic: 4938 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -134.94 48.94 1 1.00e+01 1.00e-02 3.29e+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 -134.90 48.90 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -134.89 48.89 1 1.00e+01 1.00e-02 3.29e+01 ... (remaining 8319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2044 0.119 - 0.239: 545 0.239 - 0.358: 36 0.358 - 0.478: 0 0.478 - 0.597: 3 Chirality restraints: 2628 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.00e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 ... (remaining 2625 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.064 2.00e-02 2.50e+03 6.70e-02 5.62e+01 pdb=" CG ASN F 611 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG F 703 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.064 2.00e-02 2.50e+03 6.70e-02 5.60e+01 pdb=" CG ASN B 611 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG B 703 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.064 2.00e-02 2.50e+03 6.69e-02 5.59e+01 pdb=" CG ASN D 611 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.105 2.00e-02 2.50e+03 pdb=" C1 NAG D 703 " -0.080 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3526 2.78 - 3.31: 13398 3.31 - 3.84: 24752 3.84 - 4.37: 29411 4.37 - 4.90: 46903 Nonbonded interactions: 117990 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.248 3.040 nonbonded pdb=" N ASN C 355 " pdb=" OD1 ASN C 355 " model vdw 2.391 3.120 nonbonded pdb=" N ASN E 355 " pdb=" OD1 ASN E 355 " model vdw 2.391 3.120 ... (remaining 117985 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.680 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.020 0.113 15336 Z= 1.099 Angle : 1.717 8.904 21009 Z= 1.069 Chirality : 0.100 0.597 2628 Planarity : 0.009 0.039 2484 Dihedral : 10.162 81.867 5025 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.20 % Allowed : 0.39 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1674 helix: -0.13 (0.24), residues: 420 sheet: 1.34 (0.22), residues: 411 loop : 0.79 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 192 TYR 0.068 0.008 TYR B 638 PHE 0.028 0.006 PHE A 383 TRP 0.050 0.010 TRP E 96 HIS 0.008 0.003 HIS B 585 Details of bonding type rmsd/Z covalent geometry : bond 0.02027 / 1.09 (15201) covalent geometry : angle 1.69404 / 1.07 (20637) SS BOND : bond 0.02761 / 1.91 ( 33) SS BOND : angle 2.49081 / 1.76 ( 66) hydrogen bonds : bond 0.16540 / 11.00 ( 555) hydrogen bonds : angle 7.35106 / 5.31 ( 1791) link_ALPHA1-3 : bond 0.04000 / 2.01 ( 3) link_ALPHA1-3 : angle 3.54710 / 2.42 ( 9) link_ALPHA1-6 : bond 0.02879 / 1.44 ( 3) link_ALPHA1-6 : angle 3.07845 / 2.11 ( 9) link_BETA1-4 : bond 0.03337 / 2.01 ( 33) link_BETA1-4 : angle 3.05150 / 2.12 ( 99) link_NAG-ASN : bond 0.02802 / 1.80 ( 63) link_NAG-ASN : angle 2.48207 / 1.73 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 456 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8996 (m) cc_final: 0.8668 (p) REVERT: A 180 ASP cc_start: 0.8917 (m-30) cc_final: 0.8614 (m-30) REVERT: A 195 ASN cc_start: 0.9275 (p0) cc_final: 0.9020 (p0) REVERT: A 233 PHE cc_start: 0.9195 (t80) cc_final: 0.8700 (t80) REVERT: A 251 ILE cc_start: 0.9167 (mt) cc_final: 0.8800 (mm) REVERT: A 300 ASN cc_start: 0.8908 (m-40) cc_final: 0.7758 (p0) REVERT: A 342 LEU cc_start: 0.9621 (mt) cc_final: 0.9410 (mm) REVERT: B 530 MET cc_start: 0.8896 (mtp) cc_final: 0.8489 (mtp) REVERT: B 536 THR cc_start: 0.8683 (p) cc_final: 0.8121 (t) REVERT: B 540 GLN cc_start: 0.9170 (mp-120) cc_final: 0.8878 (mp10) REVERT: B 543 ASN cc_start: 0.8475 (m-40) cc_final: 0.7974 (t0) REVERT: B 591 GLN cc_start: 0.9328 (tt0) cc_final: 0.8873 (tt0) REVERT: B 615 SER cc_start: 0.8959 (t) cc_final: 0.8650 (m) REVERT: B 617 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7046 (mmm-85) REVERT: B 618 ASN cc_start: 0.6401 (m110) cc_final: 0.6177 (m110) REVERT: B 643 TYR cc_start: 0.8850 (m-10) cc_final: 0.8626 (m-10) REVERT: C 51 THR cc_start: 0.9008 (m) cc_final: 0.8627 (p) REVERT: C 180 ASP cc_start: 0.8995 (m-30) cc_final: 0.8769 (m-30) REVERT: C 195 ASN cc_start: 0.9257 (p0) cc_final: 0.8997 (p0) REVERT: C 233 PHE cc_start: 0.9200 (t80) cc_final: 0.8902 (t80) REVERT: C 251 ILE cc_start: 0.9153 (mt) cc_final: 0.8793 (mm) REVERT: C 300 ASN cc_start: 0.8930 (m-40) cc_final: 0.7874 (p0) REVERT: C 342 LEU cc_start: 0.9628 (mt) cc_final: 0.9342 (mm) REVERT: C 423 ILE cc_start: 0.9534 (mt) cc_final: 0.9267 (mt) REVERT: D 536 THR cc_start: 0.8298 (p) cc_final: 0.7769 (t) REVERT: D 540 GLN cc_start: 0.9228 (mp-120) cc_final: 0.8890 (mp10) REVERT: D 543 ASN cc_start: 0.8388 (m-40) cc_final: 0.7782 (t0) REVERT: D 614 TRP cc_start: 0.8207 (m-10) cc_final: 0.7734 (m-10) REVERT: D 615 SER cc_start: 0.9012 (t) cc_final: 0.8630 (m) REVERT: D 617 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7205 (mmm-85) REVERT: E 51 THR cc_start: 0.9040 (m) cc_final: 0.8689 (p) REVERT: E 180 ASP cc_start: 0.9083 (m-30) cc_final: 0.8811 (m-30) REVERT: E 195 ASN cc_start: 0.9224 (p0) cc_final: 0.9006 (p0) REVERT: E 233 PHE cc_start: 0.9110 (t80) cc_final: 0.8641 (t80) REVERT: E 256 SER cc_start: 0.8245 (p) cc_final: 0.7784 (p) REVERT: E 300 ASN cc_start: 0.8959 (m-40) cc_final: 0.8691 (m-40) REVERT: E 342 LEU cc_start: 0.9625 (mt) cc_final: 0.9420 (mm) REVERT: F 530 MET cc_start: 0.8869 (mtp) cc_final: 0.8473 (mtp) REVERT: F 536 THR cc_start: 0.8654 (p) cc_final: 0.8041 (t) REVERT: F 540 GLN cc_start: 0.9253 (mp-120) cc_final: 0.8871 (mp10) REVERT: F 543 ASN cc_start: 0.8447 (m-40) cc_final: 0.8157 (t0) REVERT: F 615 SER cc_start: 0.8697 (t) cc_final: 0.8389 (m) REVERT: F 617 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.7116 (mmm-85) REVERT: F 643 TYR cc_start: 0.8769 (m-10) cc_final: 0.8232 (m-10) outliers start: 3 outliers final: 3 residues processed: 459 average time/residue: 0.1199 time to fit residues: 82.0767 Evaluate side-chains 266 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN A 422 GLN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 188 ASN C 422 GLN D 630 GLN E 185 ASN E 188 ASN E 422 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.082851 restraints weight = 30301.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.085676 restraints weight = 18762.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.087659 restraints weight = 13886.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.088984 restraints weight = 11378.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.089834 restraints weight = 9972.905| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15336 Z= 0.239 Angle : 0.823 9.500 21009 Z= 0.405 Chirality : 0.047 0.258 2628 Planarity : 0.005 0.058 2484 Dihedral : 5.011 22.012 1809 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.46 % Allowed : 2.17 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1674 helix: 1.38 (0.26), residues: 393 sheet: 1.43 (0.24), residues: 411 loop : 0.46 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 617 TYR 0.018 0.002 TYR D 643 PHE 0.014 0.002 PHE C 176 TRP 0.036 0.002 TRP A 479 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (15201) covalent geometry : angle 0.76010 / 0.39 (20637) SS BOND : bond 0.00294 / 0.18 ( 33) SS BOND : angle 1.48939 / 1.16 ( 66) hydrogen bonds : bond 0.06072 / 3.97 ( 555) hydrogen bonds : angle 5.63552 / 4.06 ( 1791) link_ALPHA1-3 : bond 0.00255 / 0.13 ( 3) link_ALPHA1-3 : angle 2.47861 / 1.71 ( 9) link_ALPHA1-6 : bond 0.00475 / 0.24 ( 3) link_ALPHA1-6 : angle 1.61957 / 1.17 ( 9) link_BETA1-4 : bond 0.00487 / 0.28 ( 33) link_BETA1-4 : angle 1.95515 / 1.43 ( 99) link_NAG-ASN : bond 0.00410 / 0.26 ( 63) link_NAG-ASN : angle 3.00115 / 2.12 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 328 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8978 (m) cc_final: 0.8455 (p) REVERT: A 87 GLU cc_start: 0.8335 (tt0) cc_final: 0.8109 (tp30) REVERT: A 180 ASP cc_start: 0.9124 (m-30) cc_final: 0.8871 (m-30) REVERT: A 217 TYR cc_start: 0.8939 (m-80) cc_final: 0.8411 (m-80) REVERT: A 256 SER cc_start: 0.8213 (p) cc_final: 0.7904 (p) REVERT: A 479 TRP cc_start: 0.8376 (m-10) cc_final: 0.8115 (m-10) REVERT: B 536 THR cc_start: 0.8573 (p) cc_final: 0.8147 (t) REVERT: B 542 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7590 (ttm170) REVERT: B 543 ASN cc_start: 0.8398 (m-40) cc_final: 0.7956 (t0) REVERT: B 615 SER cc_start: 0.8644 (t) cc_final: 0.8226 (m) REVERT: B 638 TYR cc_start: 0.8581 (m-80) cc_final: 0.8294 (m-10) REVERT: B 656 ASN cc_start: 0.8725 (m-40) cc_final: 0.8440 (m110) REVERT: C 87 GLU cc_start: 0.8356 (tt0) cc_final: 0.8111 (tp30) REVERT: C 256 SER cc_start: 0.8229 (p) cc_final: 0.7880 (p) REVERT: C 300 ASN cc_start: 0.8132 (m-40) cc_final: 0.7777 (m-40) REVERT: C 356 ASN cc_start: 0.8379 (p0) cc_final: 0.8170 (p0) REVERT: C 479 TRP cc_start: 0.8464 (m-10) cc_final: 0.7933 (m-10) REVERT: D 536 THR cc_start: 0.8398 (p) cc_final: 0.8090 (t) REVERT: D 543 ASN cc_start: 0.8419 (m-40) cc_final: 0.7864 (t0) REVERT: D 615 SER cc_start: 0.8644 (t) cc_final: 0.8183 (m) REVERT: D 632 ASP cc_start: 0.9111 (t70) cc_final: 0.8892 (t0) REVERT: D 638 TYR cc_start: 0.8485 (m-80) cc_final: 0.8272 (m-10) REVERT: E 51 THR cc_start: 0.9088 (m) cc_final: 0.8679 (p) REVERT: E 180 ASP cc_start: 0.9174 (m-30) cc_final: 0.8841 (m-30) REVERT: E 256 SER cc_start: 0.8310 (p) cc_final: 0.8022 (p) REVERT: E 479 TRP cc_start: 0.8442 (m-10) cc_final: 0.8074 (m-10) REVERT: F 536 THR cc_start: 0.8477 (p) cc_final: 0.8225 (t) REVERT: F 543 ASN cc_start: 0.8459 (m-40) cc_final: 0.8178 (t0) REVERT: F 615 SER cc_start: 0.8555 (t) cc_final: 0.8342 (m) REVERT: F 617 ARG cc_start: 0.7907 (ttm-80) cc_final: 0.7673 (mmm-85) REVERT: F 621 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7784 (tm-30) REVERT: F 638 TYR cc_start: 0.8314 (m-80) cc_final: 0.7974 (m-10) outliers start: 7 outliers final: 1 residues processed: 332 average time/residue: 0.1086 time to fit residues: 56.3848 Evaluate side-chains 241 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 30 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS A 99 ASN A 170 GLN A 188 ASN A 216 HIS B 570 HIS B 658 GLN C 85 HIS C 170 GLN C 216 HIS D 570 HIS E 85 HIS E 170 GLN E 216 HIS F 570 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.076814 restraints weight = 31083.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.079521 restraints weight = 18945.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.081355 restraints weight = 13885.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.082595 restraints weight = 11405.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.083358 restraints weight = 10023.334| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15336 Z= 0.322 Angle : 0.873 13.267 21009 Z= 0.433 Chirality : 0.050 0.258 2628 Planarity : 0.005 0.058 2484 Dihedral : 5.406 22.157 1809 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.52 % Allowed : 3.02 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1674 helix: 1.00 (0.27), residues: 420 sheet: 1.13 (0.24), residues: 441 loop : -0.24 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 480 TYR 0.025 0.002 TYR C 217 PHE 0.015 0.002 PHE E 176 TRP 0.040 0.002 TRP A 479 HIS 0.007 0.002 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.32 (15201) covalent geometry : angle 0.81649 / 0.42 (20637) SS BOND : bond 0.00773 / 0.43 ( 33) SS BOND : angle 2.45348 / 1.77 ( 66) hydrogen bonds : bond 0.06005 / 3.98 ( 555) hydrogen bonds : angle 5.42529 / 3.90 ( 1791) link_ALPHA1-3 : bond 0.00170 / 0.08 ( 3) link_ALPHA1-3 : angle 1.75035 / 1.23 ( 9) link_ALPHA1-6 : bond 0.00420 / 0.21 ( 3) link_ALPHA1-6 : angle 1.62424 / 1.19 ( 9) link_BETA1-4 : bond 0.00280 / 0.17 ( 33) link_BETA1-4 : angle 1.66840 / 1.21 ( 99) link_NAG-ASN : bond 0.00575 / 0.37 ( 63) link_NAG-ASN : angle 2.84658 / 1.96 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 266 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9184 (m) cc_final: 0.8832 (p) REVERT: A 180 ASP cc_start: 0.9205 (m-30) cc_final: 0.8959 (m-30) REVERT: A 256 SER cc_start: 0.8580 (p) cc_final: 0.8305 (p) REVERT: B 536 THR cc_start: 0.8829 (p) cc_final: 0.8489 (t) REVERT: B 615 SER cc_start: 0.8841 (t) cc_final: 0.8296 (m) REVERT: C 256 SER cc_start: 0.8803 (p) cc_final: 0.8435 (p) REVERT: C 342 LEU cc_start: 0.9346 (mm) cc_final: 0.8736 (tp) REVERT: D 536 THR cc_start: 0.8720 (p) cc_final: 0.8388 (t) REVERT: D 615 SER cc_start: 0.8820 (t) cc_final: 0.8359 (m) REVERT: D 617 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7539 (mtp180) REVERT: D 638 TYR cc_start: 0.8491 (m-80) cc_final: 0.8093 (m-10) REVERT: E 51 THR cc_start: 0.9257 (m) cc_final: 0.8836 (p) REVERT: E 161 MET cc_start: 0.9121 (tpp) cc_final: 0.8881 (tpt) REVERT: E 180 ASP cc_start: 0.9203 (m-30) cc_final: 0.8763 (m-30) REVERT: E 217 TYR cc_start: 0.9026 (m-80) cc_final: 0.8818 (m-80) REVERT: E 256 SER cc_start: 0.8663 (p) cc_final: 0.8290 (p) REVERT: E 342 LEU cc_start: 0.9391 (mm) cc_final: 0.8729 (tp) REVERT: E 423 ILE cc_start: 0.9500 (mt) cc_final: 0.9168 (mm) REVERT: E 479 TRP cc_start: 0.8663 (m-10) cc_final: 0.8304 (m-10) REVERT: F 536 THR cc_start: 0.8775 (p) cc_final: 0.8459 (t) REVERT: F 615 SER cc_start: 0.8756 (t) cc_final: 0.8422 (m) REVERT: F 617 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7669 (mmm-85) REVERT: F 621 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8115 (tm-30) REVERT: F 626 MET cc_start: 0.8747 (mmm) cc_final: 0.8129 (mmm) REVERT: F 632 ASP cc_start: 0.9275 (t0) cc_final: 0.8937 (t0) REVERT: F 638 TYR cc_start: 0.8286 (m-80) cc_final: 0.7882 (m-10) outliers start: 8 outliers final: 2 residues processed: 271 average time/residue: 0.1094 time to fit residues: 46.7829 Evaluate side-chains 206 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 152 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.079402 restraints weight = 30290.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.082181 restraints weight = 18520.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.084075 restraints weight = 13558.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.085336 restraints weight = 11087.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.086106 restraints weight = 9735.311| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15336 Z= 0.176 Angle : 0.711 13.659 21009 Z= 0.352 Chirality : 0.046 0.301 2628 Planarity : 0.004 0.049 2484 Dihedral : 5.041 22.005 1809 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.26 % Allowed : 2.17 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1674 helix: 1.60 (0.27), residues: 393 sheet: 0.97 (0.24), residues: 423 loop : -0.18 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 542 TYR 0.033 0.002 TYR B 638 PHE 0.011 0.001 PHE C 176 TRP 0.033 0.002 TRP A 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (15201) covalent geometry : angle 0.65798 / 0.34 (20637) SS BOND : bond 0.00257 / 0.15 ( 33) SS BOND : angle 2.55998 / 2.01 ( 66) hydrogen bonds : bond 0.05034 / 3.35 ( 555) hydrogen bonds : angle 5.06630 / 3.63 ( 1791) link_ALPHA1-3 : bond 0.00357 / 0.18 ( 3) link_ALPHA1-3 : angle 1.92999 / 1.34 ( 9) link_ALPHA1-6 : bond 0.00394 / 0.20 ( 3) link_ALPHA1-6 : angle 1.53751 / 1.09 ( 9) link_BETA1-4 : bond 0.00374 / 0.22 ( 33) link_BETA1-4 : angle 1.27749 / 0.92 ( 99) link_NAG-ASN : bond 0.00275 / 0.17 ( 63) link_NAG-ASN : angle 2.32602 / 1.61 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 256 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9276 (m) cc_final: 0.8834 (p) REVERT: A 180 ASP cc_start: 0.9146 (m-30) cc_final: 0.8943 (m-30) REVERT: A 256 SER cc_start: 0.8384 (p) cc_final: 0.8093 (p) REVERT: B 536 THR cc_start: 0.8870 (p) cc_final: 0.8542 (t) REVERT: B 615 SER cc_start: 0.8927 (t) cc_final: 0.8444 (m) REVERT: C 51 THR cc_start: 0.9166 (m) cc_final: 0.8860 (p) REVERT: C 114 GLN cc_start: 0.8568 (tp-100) cc_final: 0.8355 (tp40) REVERT: C 256 SER cc_start: 0.8626 (p) cc_final: 0.8299 (p) REVERT: C 284 ILE cc_start: 0.9468 (mt) cc_final: 0.8953 (tt) REVERT: C 342 LEU cc_start: 0.9273 (mm) cc_final: 0.8640 (tp) REVERT: D 614 TRP cc_start: 0.8525 (m-10) cc_final: 0.7547 (m-10) REVERT: D 615 SER cc_start: 0.8804 (t) cc_final: 0.8117 (m) REVERT: D 617 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7190 (mtm180) REVERT: D 638 TYR cc_start: 0.8319 (m-80) cc_final: 0.7947 (m-10) REVERT: E 51 THR cc_start: 0.9311 (m) cc_final: 0.8916 (p) REVERT: E 104 MET cc_start: 0.8939 (tpp) cc_final: 0.8738 (tpp) REVERT: E 108 ILE cc_start: 0.9045 (tt) cc_final: 0.8812 (tt) REVERT: E 114 GLN cc_start: 0.8662 (tp40) cc_final: 0.8285 (tp40) REVERT: E 161 MET cc_start: 0.9174 (tpp) cc_final: 0.8944 (tpt) REVERT: E 180 ASP cc_start: 0.9203 (m-30) cc_final: 0.8772 (m-30) REVERT: E 256 SER cc_start: 0.8555 (p) cc_final: 0.8210 (p) REVERT: E 423 ILE cc_start: 0.9530 (mt) cc_final: 0.9247 (mm) REVERT: F 536 THR cc_start: 0.8694 (p) cc_final: 0.8489 (t) REVERT: F 538 THR cc_start: 0.8968 (p) cc_final: 0.8449 (p) REVERT: F 615 SER cc_start: 0.8672 (t) cc_final: 0.8305 (m) REVERT: F 621 GLU cc_start: 0.8725 (tm-30) cc_final: 0.7815 (tp30) REVERT: F 626 MET cc_start: 0.8757 (mmm) cc_final: 0.8308 (mmm) REVERT: F 638 TYR cc_start: 0.8139 (m-80) cc_final: 0.7625 (m-10) outliers start: 4 outliers final: 2 residues processed: 258 average time/residue: 0.1067 time to fit residues: 43.5294 Evaluate side-chains 216 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 128 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.078509 restraints weight = 30368.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.081247 restraints weight = 18667.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.083069 restraints weight = 13714.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.084211 restraints weight = 11299.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.085118 restraints weight = 9938.727| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 15336 Z= 0.198 Angle : 0.709 12.330 21009 Z= 0.351 Chirality : 0.046 0.304 2628 Planarity : 0.004 0.048 2484 Dihedral : 5.020 22.280 1809 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1674 helix: 1.65 (0.27), residues: 393 sheet: 0.89 (0.25), residues: 423 loop : -0.20 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 617 TYR 0.016 0.002 TYR B 638 PHE 0.010 0.001 PHE C 176 TRP 0.031 0.002 TRP E 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (15201) covalent geometry : angle 0.65669 / 0.34 (20637) SS BOND : bond 0.00566 / 0.32 ( 33) SS BOND : angle 2.62658 / 2.09 ( 66) hydrogen bonds : bond 0.04913 / 3.29 ( 555) hydrogen bonds : angle 4.94189 / 3.54 ( 1791) link_ALPHA1-3 : bond 0.00327 / 0.16 ( 3) link_ALPHA1-3 : angle 1.79963 / 1.24 ( 9) link_ALPHA1-6 : bond 0.00370 / 0.19 ( 3) link_ALPHA1-6 : angle 1.51027 / 1.09 ( 9) link_BETA1-4 : bond 0.00262 / 0.16 ( 33) link_BETA1-4 : angle 1.28713 / 0.92 ( 99) link_NAG-ASN : bond 0.00306 / 0.19 ( 63) link_NAG-ASN : angle 2.28057 / 1.55 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9345 (m) cc_final: 0.9060 (p) REVERT: A 180 ASP cc_start: 0.9175 (m-30) cc_final: 0.8961 (m-30) REVERT: A 256 SER cc_start: 0.8477 (p) cc_final: 0.8168 (p) REVERT: B 530 MET cc_start: 0.8678 (mtp) cc_final: 0.8315 (mmm) REVERT: B 536 THR cc_start: 0.8602 (p) cc_final: 0.8191 (t) REVERT: B 540 GLN cc_start: 0.9062 (mp-120) cc_final: 0.8703 (mp10) REVERT: B 615 SER cc_start: 0.8727 (t) cc_final: 0.8202 (m) REVERT: C 51 THR cc_start: 0.9312 (m) cc_final: 0.9007 (p) REVERT: C 114 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8379 (tp40) REVERT: C 256 SER cc_start: 0.8630 (p) cc_final: 0.8276 (p) REVERT: C 284 ILE cc_start: 0.9504 (mt) cc_final: 0.9050 (tt) REVERT: C 434 MET cc_start: 0.8641 (mtp) cc_final: 0.8295 (mtm) REVERT: C 486 TYR cc_start: 0.8623 (m-80) cc_final: 0.8229 (m-80) REVERT: D 535 MET cc_start: 0.8666 (mmt) cc_final: 0.8452 (mmt) REVERT: D 540 GLN cc_start: 0.9016 (mp-120) cc_final: 0.8587 (mp10) REVERT: D 615 SER cc_start: 0.8757 (t) cc_final: 0.8059 (m) REVERT: D 617 ARG cc_start: 0.7456 (mtp180) cc_final: 0.6977 (mmm-85) REVERT: D 632 ASP cc_start: 0.9216 (t0) cc_final: 0.8975 (t0) REVERT: E 51 THR cc_start: 0.9394 (m) cc_final: 0.9070 (p) REVERT: E 161 MET cc_start: 0.9094 (tpp) cc_final: 0.8857 (tpt) REVERT: E 180 ASP cc_start: 0.9152 (m-30) cc_final: 0.8774 (m-30) REVERT: E 217 TYR cc_start: 0.8894 (m-80) cc_final: 0.8547 (m-80) REVERT: E 256 SER cc_start: 0.8651 (p) cc_final: 0.8295 (p) REVERT: E 423 ILE cc_start: 0.9546 (mt) cc_final: 0.9264 (mm) REVERT: F 530 MET cc_start: 0.8596 (mtp) cc_final: 0.8040 (mmt) REVERT: F 536 THR cc_start: 0.8592 (p) cc_final: 0.8235 (t) REVERT: F 615 SER cc_start: 0.8752 (t) cc_final: 0.8261 (m) REVERT: F 617 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7358 (mtm180) REVERT: F 621 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8131 (tm-30) REVERT: F 632 ASP cc_start: 0.9179 (t0) cc_final: 0.8891 (t0) REVERT: F 633 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8858 (tptm) REVERT: F 638 TYR cc_start: 0.8135 (m-80) cc_final: 0.7658 (m-10) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1080 time to fit residues: 41.5249 Evaluate side-chains 205 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS B 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.078896 restraints weight = 30270.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.081621 restraints weight = 18695.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.083493 restraints weight = 13793.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.084733 restraints weight = 11318.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.085539 restraints weight = 9962.665| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15336 Z= 0.183 Angle : 0.695 12.407 21009 Z= 0.343 Chirality : 0.046 0.292 2628 Planarity : 0.004 0.058 2484 Dihedral : 4.990 24.804 1809 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1674 helix: 1.64 (0.27), residues: 393 sheet: 0.98 (0.25), residues: 417 loop : -0.22 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.016 0.001 TYR B 638 PHE 0.009 0.001 PHE C 176 TRP 0.035 0.002 TRP C 112 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (15201) covalent geometry : angle 0.64726 / 0.33 (20637) SS BOND : bond 0.00557 / 0.31 ( 33) SS BOND : angle 2.62388 / 2.08 ( 66) hydrogen bonds : bond 0.04745 / 3.16 ( 555) hydrogen bonds : angle 4.86046 / 3.47 ( 1791) link_ALPHA1-3 : bond 0.00310 / 0.16 ( 3) link_ALPHA1-3 : angle 1.82420 / 1.24 ( 9) link_ALPHA1-6 : bond 0.00381 / 0.19 ( 3) link_ALPHA1-6 : angle 1.50951 / 1.08 ( 9) link_BETA1-4 : bond 0.00341 / 0.20 ( 33) link_BETA1-4 : angle 1.23878 / 0.88 ( 99) link_NAG-ASN : bond 0.00250 / 0.16 ( 63) link_NAG-ASN : angle 2.10834 / 1.43 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8448 (mmm) cc_final: 0.8037 (mmm) REVERT: A 195 ASN cc_start: 0.8932 (p0) cc_final: 0.8719 (p0) REVERT: A 256 SER cc_start: 0.8339 (p) cc_final: 0.7944 (p) REVERT: B 530 MET cc_start: 0.8590 (mtp) cc_final: 0.8332 (mmm) REVERT: B 615 SER cc_start: 0.8605 (t) cc_final: 0.8142 (m) REVERT: C 51 THR cc_start: 0.9350 (m) cc_final: 0.9056 (p) REVERT: C 114 GLN cc_start: 0.8577 (tp-100) cc_final: 0.8360 (tp40) REVERT: C 256 SER cc_start: 0.8580 (p) cc_final: 0.8249 (p) REVERT: C 284 ILE cc_start: 0.9528 (mt) cc_final: 0.9102 (tt) REVERT: C 486 TYR cc_start: 0.8677 (m-80) cc_final: 0.8416 (m-80) REVERT: D 530 MET cc_start: 0.8687 (mtp) cc_final: 0.8337 (mmt) REVERT: D 540 GLN cc_start: 0.9111 (mp-120) cc_final: 0.8708 (mp10) REVERT: D 615 SER cc_start: 0.8610 (t) cc_final: 0.7899 (m) REVERT: D 647 GLU cc_start: 0.7613 (pt0) cc_final: 0.7298 (pt0) REVERT: E 51 THR cc_start: 0.9418 (m) cc_final: 0.9092 (p) REVERT: E 161 MET cc_start: 0.8911 (tpp) cc_final: 0.8685 (tpp) REVERT: E 180 ASP cc_start: 0.9143 (m-30) cc_final: 0.8793 (m-30) REVERT: E 210 PHE cc_start: 0.9054 (m-80) cc_final: 0.8464 (m-80) REVERT: E 217 TYR cc_start: 0.8829 (m-80) cc_final: 0.8466 (m-80) REVERT: E 256 SER cc_start: 0.8627 (p) cc_final: 0.8282 (p) REVERT: E 381 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8151 (mm-30) REVERT: E 423 ILE cc_start: 0.9524 (mt) cc_final: 0.9285 (mm) REVERT: F 530 MET cc_start: 0.8593 (mtp) cc_final: 0.7973 (mmt) REVERT: F 535 MET cc_start: 0.8929 (mmp) cc_final: 0.8677 (mmt) REVERT: F 536 THR cc_start: 0.8701 (p) cc_final: 0.8378 (t) REVERT: F 615 SER cc_start: 0.8763 (t) cc_final: 0.8264 (m) REVERT: F 632 ASP cc_start: 0.9182 (t0) cc_final: 0.8934 (t0) REVERT: F 633 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8859 (tptm) REVERT: F 638 TYR cc_start: 0.8076 (m-80) cc_final: 0.7572 (m-10) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1036 time to fit residues: 39.5788 Evaluate side-chains 195 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 0.0870 chunk 110 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS E 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.080533 restraints weight = 29978.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.083323 restraints weight = 18272.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.085218 restraints weight = 13369.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.086439 restraints weight = 10945.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087304 restraints weight = 9633.261| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15336 Z= 0.138 Angle : 0.652 12.196 21009 Z= 0.324 Chirality : 0.045 0.266 2628 Planarity : 0.004 0.045 2484 Dihedral : 4.894 27.456 1809 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1674 helix: 1.61 (0.27), residues: 396 sheet: 1.00 (0.25), residues: 411 loop : -0.19 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 542 TYR 0.016 0.001 TYR B 638 PHE 0.009 0.001 PHE C 176 TRP 0.031 0.001 TRP E 479 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15201) covalent geometry : angle 0.60683 / 0.31 (20637) SS BOND : bond 0.00554 / 0.31 ( 33) SS BOND : angle 2.48905 / 2.00 ( 66) hydrogen bonds : bond 0.04398 / 2.91 ( 555) hydrogen bonds : angle 4.77535 / 3.40 ( 1791) link_ALPHA1-3 : bond 0.00415 / 0.21 ( 3) link_ALPHA1-3 : angle 1.64804 / 1.12 ( 9) link_ALPHA1-6 : bond 0.00410 / 0.21 ( 3) link_ALPHA1-6 : angle 1.43791 / 1.02 ( 9) link_BETA1-4 : bond 0.00334 / 0.20 ( 33) link_BETA1-4 : angle 1.11122 / 0.78 ( 99) link_NAG-ASN : bond 0.00176 / 0.11 ( 63) link_NAG-ASN : angle 2.01820 / 1.36 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9277 (tpp) cc_final: 0.8923 (tpt) REVERT: A 180 ASP cc_start: 0.9130 (m-30) cc_final: 0.8345 (m-30) REVERT: A 195 ASN cc_start: 0.8848 (p0) cc_final: 0.8615 (p0) REVERT: A 256 SER cc_start: 0.8382 (p) cc_final: 0.8071 (p) REVERT: A 423 ILE cc_start: 0.9538 (mt) cc_final: 0.9225 (mt) REVERT: B 615 SER cc_start: 0.8496 (t) cc_final: 0.7921 (m) REVERT: B 617 ARG cc_start: 0.7348 (mtp180) cc_final: 0.6962 (mtp180) REVERT: C 51 THR cc_start: 0.9304 (m) cc_final: 0.9065 (p) REVERT: C 114 GLN cc_start: 0.8540 (tp-100) cc_final: 0.8316 (tp40) REVERT: C 247 CYS cc_start: 0.5370 (p) cc_final: 0.5049 (p) REVERT: C 256 SER cc_start: 0.8489 (p) cc_final: 0.8182 (p) REVERT: C 284 ILE cc_start: 0.9553 (mt) cc_final: 0.9188 (tt) REVERT: D 530 MET cc_start: 0.8677 (mtp) cc_final: 0.8384 (mmt) REVERT: D 615 SER cc_start: 0.8519 (t) cc_final: 0.7785 (m) REVERT: D 654 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7410 (mp0) REVERT: E 51 THR cc_start: 0.9371 (m) cc_final: 0.8900 (p) REVERT: E 180 ASP cc_start: 0.9159 (m-30) cc_final: 0.8806 (m-30) REVERT: E 195 ASN cc_start: 0.8723 (p0) cc_final: 0.8323 (p0) REVERT: E 256 SER cc_start: 0.8628 (p) cc_final: 0.8281 (p) REVERT: E 423 ILE cc_start: 0.9543 (mt) cc_final: 0.9314 (mm) REVERT: F 530 MET cc_start: 0.8483 (mtp) cc_final: 0.7804 (mtp) REVERT: F 535 MET cc_start: 0.8931 (mmp) cc_final: 0.8640 (mmt) REVERT: F 536 THR cc_start: 0.8696 (p) cc_final: 0.8419 (t) REVERT: F 603 ILE cc_start: 0.9434 (mp) cc_final: 0.9151 (mm) REVERT: F 615 SER cc_start: 0.8584 (t) cc_final: 0.8045 (m) REVERT: F 621 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8407 (tm-30) REVERT: F 638 TYR cc_start: 0.8015 (m-80) cc_final: 0.7519 (m-10) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1059 time to fit residues: 42.0239 Evaluate side-chains 199 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 119 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 85 HIS E 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.080086 restraints weight = 30235.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.082846 restraints weight = 18580.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.084746 restraints weight = 13604.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.085763 restraints weight = 11109.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.086774 restraints weight = 9846.659| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15336 Z= 0.156 Angle : 0.659 11.792 21009 Z= 0.329 Chirality : 0.045 0.275 2628 Planarity : 0.004 0.070 2484 Dihedral : 4.938 31.461 1809 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.20), residues: 1674 helix: 1.56 (0.27), residues: 393 sheet: 0.88 (0.25), residues: 399 loop : -0.22 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 542 TYR 0.028 0.001 TYR D 638 PHE 0.008 0.001 PHE A 176 TRP 0.047 0.002 TRP A 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (15201) covalent geometry : angle 0.61357 / 0.32 (20637) SS BOND : bond 0.00521 / 0.29 ( 33) SS BOND : angle 2.62523 / 2.01 ( 66) hydrogen bonds : bond 0.04530 / 3.00 ( 555) hydrogen bonds : angle 4.75132 / 3.38 ( 1791) link_ALPHA1-3 : bond 0.00386 / 0.19 ( 3) link_ALPHA1-3 : angle 1.69482 / 1.15 ( 9) link_ALPHA1-6 : bond 0.00429 / 0.22 ( 3) link_ALPHA1-6 : angle 1.47868 / 1.06 ( 9) link_BETA1-4 : bond 0.00315 / 0.19 ( 33) link_BETA1-4 : angle 1.14002 / 0.80 ( 99) link_NAG-ASN : bond 0.00220 / 0.13 ( 63) link_NAG-ASN : angle 1.95828 / 1.32 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7758 (m-90) cc_final: 0.7496 (m100) REVERT: A 100 MET cc_start: 0.8611 (mmm) cc_final: 0.8330 (mmm) REVERT: A 161 MET cc_start: 0.9277 (tpp) cc_final: 0.8918 (tpt) REVERT: A 180 ASP cc_start: 0.9136 (m-30) cc_final: 0.8328 (m-30) REVERT: A 195 ASN cc_start: 0.8833 (p0) cc_final: 0.8613 (p0) REVERT: A 256 SER cc_start: 0.8430 (p) cc_final: 0.8032 (p) REVERT: A 423 ILE cc_start: 0.9533 (mt) cc_final: 0.9238 (mt) REVERT: B 530 MET cc_start: 0.9327 (mmm) cc_final: 0.9078 (mmt) REVERT: B 654 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7852 (mp0) REVERT: C 51 THR cc_start: 0.9250 (m) cc_final: 0.9030 (p) REVERT: C 114 GLN cc_start: 0.8548 (tp-100) cc_final: 0.8307 (tp40) REVERT: C 256 SER cc_start: 0.8424 (p) cc_final: 0.8073 (p) REVERT: C 284 ILE cc_start: 0.9547 (mt) cc_final: 0.9221 (tt) REVERT: C 426 MET cc_start: 0.8524 (mmm) cc_final: 0.8321 (mmt) REVERT: D 530 MET cc_start: 0.8677 (mtp) cc_final: 0.8406 (mmm) REVERT: D 615 SER cc_start: 0.8535 (t) cc_final: 0.7727 (m) REVERT: D 632 ASP cc_start: 0.9252 (t0) cc_final: 0.9049 (t0) REVERT: E 51 THR cc_start: 0.9404 (m) cc_final: 0.9042 (p) REVERT: E 104 MET cc_start: 0.8862 (tpp) cc_final: 0.8632 (tpp) REVERT: E 180 ASP cc_start: 0.9175 (m-30) cc_final: 0.8682 (m-30) REVERT: E 195 ASN cc_start: 0.8710 (p0) cc_final: 0.8285 (p0) REVERT: E 256 SER cc_start: 0.8686 (p) cc_final: 0.8405 (p) REVERT: E 423 ILE cc_start: 0.9529 (mt) cc_final: 0.9095 (mt) REVERT: F 530 MET cc_start: 0.8464 (mtp) cc_final: 0.7861 (mtp) REVERT: F 535 MET cc_start: 0.8965 (mmp) cc_final: 0.8600 (mmt) REVERT: F 615 SER cc_start: 0.8523 (t) cc_final: 0.7964 (m) REVERT: F 621 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8182 (tm-30) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.0959 time to fit residues: 35.3354 Evaluate side-chains 191 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 116 optimal weight: 0.0470 chunk 21 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 128 optimal weight: 0.0070 overall best weight: 1.1498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.082095 restraints weight = 30042.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.084890 restraints weight = 18317.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.086810 restraints weight = 13375.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.088096 restraints weight = 10889.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.088911 restraints weight = 9516.742| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15336 Z= 0.114 Angle : 0.614 10.075 21009 Z= 0.308 Chirality : 0.044 0.222 2628 Planarity : 0.004 0.040 2484 Dihedral : 4.791 31.563 1809 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.21), residues: 1674 helix: 1.62 (0.27), residues: 393 sheet: 0.87 (0.25), residues: 405 loop : -0.20 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 542 TYR 0.029 0.001 TYR C 486 PHE 0.008 0.001 PHE A 176 TRP 0.042 0.001 TRP A 479 HIS 0.006 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (15201) covalent geometry : angle 0.57456 / 0.30 (20637) SS BOND : bond 0.00321 / 0.18 ( 33) SS BOND : angle 2.27366 / 1.76 ( 66) hydrogen bonds : bond 0.04089 / 2.69 ( 555) hydrogen bonds : angle 4.60417 / 3.26 ( 1791) link_ALPHA1-3 : bond 0.00480 / 0.24 ( 3) link_ALPHA1-3 : angle 1.55247 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00467 / 0.23 ( 3) link_ALPHA1-6 : angle 1.41248 / 1.00 ( 9) link_BETA1-4 : bond 0.00365 / 0.22 ( 33) link_BETA1-4 : angle 1.00189 / 0.70 ( 99) link_NAG-ASN : bond 0.00143 / 0.09 ( 63) link_NAG-ASN : angle 1.83974 / 1.24 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8518 (mmm) cc_final: 0.8200 (mmm) REVERT: A 161 MET cc_start: 0.9257 (tpp) cc_final: 0.8895 (tpt) REVERT: A 180 ASP cc_start: 0.9139 (m-30) cc_final: 0.8466 (m-30) REVERT: A 195 ASN cc_start: 0.8735 (p0) cc_final: 0.8485 (p0) REVERT: A 256 SER cc_start: 0.8440 (p) cc_final: 0.8060 (p) REVERT: A 423 ILE cc_start: 0.9500 (mt) cc_final: 0.9290 (mt) REVERT: C 51 THR cc_start: 0.9252 (m) cc_final: 0.8988 (p) REVERT: C 114 GLN cc_start: 0.8497 (tp-100) cc_final: 0.8259 (tp40) REVERT: C 217 TYR cc_start: 0.8640 (m-80) cc_final: 0.8417 (m-80) REVERT: C 256 SER cc_start: 0.8412 (p) cc_final: 0.8074 (p) REVERT: C 284 ILE cc_start: 0.9505 (mt) cc_final: 0.9191 (tt) REVERT: D 615 SER cc_start: 0.8462 (t) cc_final: 0.7654 (m) REVERT: D 632 ASP cc_start: 0.9237 (t0) cc_final: 0.8984 (t0) REVERT: E 51 THR cc_start: 0.9377 (m) cc_final: 0.9054 (p) REVERT: E 180 ASP cc_start: 0.9136 (m-30) cc_final: 0.8910 (m-30) REVERT: E 195 ASN cc_start: 0.8651 (p0) cc_final: 0.8440 (p0) REVERT: E 256 SER cc_start: 0.8575 (p) cc_final: 0.8235 (p) REVERT: F 530 MET cc_start: 0.8357 (mtp) cc_final: 0.7850 (mmm) REVERT: F 535 MET cc_start: 0.8960 (mmp) cc_final: 0.8651 (mmt) REVERT: F 603 ILE cc_start: 0.9402 (mp) cc_final: 0.9152 (mm) REVERT: F 615 SER cc_start: 0.8470 (t) cc_final: 0.7862 (m) REVERT: F 617 ARG cc_start: 0.7585 (mmm-85) cc_final: 0.7253 (mtp180) REVERT: F 626 MET cc_start: 0.7699 (mmm) cc_final: 0.7146 (mmm) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1010 time to fit residues: 39.2312 Evaluate side-chains 207 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 45 optimal weight: 0.0000 chunk 28 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN B 656 ASN C 105 HIS C 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.080092 restraints weight = 30488.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.082765 restraints weight = 18869.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.084617 restraints weight = 13902.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.085864 restraints weight = 11392.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.086657 restraints weight = 9998.688| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15336 Z= 0.173 Angle : 0.659 10.772 21009 Z= 0.329 Chirality : 0.045 0.237 2628 Planarity : 0.004 0.050 2484 Dihedral : 4.907 31.342 1809 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1674 helix: 1.44 (0.26), residues: 396 sheet: 0.83 (0.25), residues: 405 loop : -0.24 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 542 TYR 0.032 0.002 TYR F 638 PHE 0.007 0.001 PHE E 176 TRP 0.063 0.002 TRP A 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (15201) covalent geometry : angle 0.61648 / 0.32 (20637) SS BOND : bond 0.00457 / 0.27 ( 33) SS BOND : angle 2.43950 / 1.93 ( 66) hydrogen bonds : bond 0.04437 / 2.92 ( 555) hydrogen bonds : angle 4.70641 / 3.36 ( 1791) link_ALPHA1-3 : bond 0.00356 / 0.18 ( 3) link_ALPHA1-3 : angle 1.70391 / 1.15 ( 9) link_ALPHA1-6 : bond 0.00432 / 0.22 ( 3) link_ALPHA1-6 : angle 1.51909 / 1.09 ( 9) link_BETA1-4 : bond 0.00285 / 0.17 ( 33) link_BETA1-4 : angle 1.16512 / 0.82 ( 99) link_NAG-ASN : bond 0.00216 / 0.13 ( 63) link_NAG-ASN : angle 1.91766 / 1.30 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8463 (mmm) cc_final: 0.8176 (mmm) REVERT: A 161 MET cc_start: 0.9238 (tpp) cc_final: 0.8882 (tpt) REVERT: A 180 ASP cc_start: 0.9139 (m-30) cc_final: 0.8366 (m-30) REVERT: A 195 ASN cc_start: 0.8661 (p0) cc_final: 0.8374 (p0) REVERT: A 256 SER cc_start: 0.8508 (p) cc_final: 0.8107 (p) REVERT: A 423 ILE cc_start: 0.9521 (mt) cc_final: 0.9254 (mt) REVERT: C 51 THR cc_start: 0.9264 (m) cc_final: 0.9045 (p) REVERT: C 114 GLN cc_start: 0.8548 (tp-100) cc_final: 0.8323 (tp40) REVERT: C 217 TYR cc_start: 0.8719 (m-80) cc_final: 0.8432 (m-80) REVERT: C 256 SER cc_start: 0.8546 (p) cc_final: 0.8186 (p) REVERT: C 284 ILE cc_start: 0.9529 (mt) cc_final: 0.9230 (tt) REVERT: C 426 MET cc_start: 0.8297 (mmm) cc_final: 0.7869 (mmt) REVERT: D 530 MET cc_start: 0.9362 (mmm) cc_final: 0.9052 (mmt) REVERT: D 632 ASP cc_start: 0.9257 (t0) cc_final: 0.9016 (t0) REVERT: E 51 THR cc_start: 0.9388 (m) cc_final: 0.9056 (p) REVERT: E 104 MET cc_start: 0.8811 (tpp) cc_final: 0.8596 (tpp) REVERT: E 180 ASP cc_start: 0.9182 (m-30) cc_final: 0.8712 (m-30) REVERT: E 195 ASN cc_start: 0.8724 (p0) cc_final: 0.8293 (p0) REVERT: E 217 TYR cc_start: 0.8381 (m-80) cc_final: 0.8119 (m-80) REVERT: E 256 SER cc_start: 0.8690 (p) cc_final: 0.8374 (p) REVERT: E 423 ILE cc_start: 0.9560 (mt) cc_final: 0.9225 (mt) REVERT: E 434 MET cc_start: 0.8526 (ttm) cc_final: 0.8318 (mtp) REVERT: F 530 MET cc_start: 0.8357 (mtp) cc_final: 0.7720 (mtp) REVERT: F 614 TRP cc_start: 0.8497 (m-10) cc_final: 0.7829 (m-90) REVERT: F 615 SER cc_start: 0.8514 (t) cc_final: 0.7852 (m) REVERT: F 626 MET cc_start: 0.7801 (mmm) cc_final: 0.7320 (mmm) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.0989 time to fit residues: 35.1888 Evaluate side-chains 191 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 148 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 123 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.079385 restraints weight = 30109.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.082048 restraints weight = 18689.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.083834 restraints weight = 13772.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.085047 restraints weight = 11342.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.085847 restraints weight = 9983.211| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15336 Z= 0.188 Angle : 0.673 11.614 21009 Z= 0.336 Chirality : 0.046 0.257 2628 Planarity : 0.004 0.043 2484 Dihedral : 5.001 36.080 1809 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1674 helix: 1.46 (0.27), residues: 396 sheet: 0.59 (0.25), residues: 420 loop : -0.33 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 542 TYR 0.040 0.002 TYR F 638 PHE 0.009 0.001 PHE A 176 TRP 0.062 0.002 TRP A 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (15201) covalent geometry : angle 0.63092 / 0.32 (20637) SS BOND : bond 0.00437 / 0.24 ( 33) SS BOND : angle 2.61283 / 2.09 ( 66) hydrogen bonds : bond 0.04537 / 2.99 ( 555) hydrogen bonds : angle 4.71586 / 3.36 ( 1791) link_ALPHA1-3 : bond 0.00291 / 0.15 ( 3) link_ALPHA1-3 : angle 1.76670 / 1.19 ( 9) link_ALPHA1-6 : bond 0.00411 / 0.21 ( 3) link_ALPHA1-6 : angle 1.55201 / 1.11 ( 9) link_BETA1-4 : bond 0.00291 / 0.17 ( 33) link_BETA1-4 : angle 1.19398 / 0.84 ( 99) link_NAG-ASN : bond 0.00234 / 0.14 ( 63) link_NAG-ASN : angle 1.86813 / 1.27 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.26 seconds wall clock time: 37 minutes 58.30 seconds (2278.30 seconds total)