Starting phenix.real_space_refine on Sun Jul 5 13:06:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d5a_27207/07_2026/8d5a_27207.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d5a_27207/07_2026/8d5a_27207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d5a_27207/07_2026/8d5a_27207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d5a_27207/07_2026/8d5a_27207.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d5a_27207/07_2026/8d5a_27207.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d5a_27207/07_2026/8d5a_27207.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d5a_27207/07_2026/8d5a_27207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d5a_27207/07_2026/8d5a_27207.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17622 2.51 5 N 4487 2.21 5 O 5482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 171 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27711 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8773 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 52, 'TRANS': 1065} Chain breaks: 4 Chain: "B" Number of atoms: 8822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1125, 8822 Classifications: {'peptide': 1125} Link IDs: {'PTRANS': 52, 'TRANS': 1072} Chain breaks: 3 Chain: "C" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8796 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 52, 'TRANS': 1069} Chain breaks: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.57, per 1000 atoms: 0.24 Number of scatterers: 27711 At special positions: 0 Unit cell: (146.08, 151.06, 205.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5482 8.00 N 4487 7.00 C 17622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=1.99 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.01 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.00 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.01 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.06 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG F 2 " - " MAN F 3 " " NAG H 2 " - " MAN H 3 " " NAG I 2 " - " MAN I 3 " " NAG K 2 " - " MAN K 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG W 2 " - " MAN W 3 " " NAG Z 2 " - " MAN Z 3 " " NAG b 2 " - " MAN b 3 " " NAG c 2 " - " MAN c 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG 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 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 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 " BETA1-6 " NAG J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 331 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 331 " " NAG B1403 " - " ASN B 343 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 331 " " NAG C1403 " - " ASN C 603 " " NAG C1404 " - " ASN C 657 " " NAG C1405 " - " ASN C 709 " " NAG C1406 " - " ASN C1158 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 616 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 282 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1074 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 45 sheets defined 27.1% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.619A pdb=" N LEU A 216 " --> pdb=" O GLY A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.602A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.802A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.735A pdb=" N ALA A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.593A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.544A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.971A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.743A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.449A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.803A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.313A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.580A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.336A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.452A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.569A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.248A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.248A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.762A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.842A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.680A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.203A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.885A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.713A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.913A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.543A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.657A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.310A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.665A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.654A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1159 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.123A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 403 through 411 removed outlier: 4.626A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.829A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 639 removed outlier: 3.610A pdb=" N TYR C 636 " --> pdb=" O TRP C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.337A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.677A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.687A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 848 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.716A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.104A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.845A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.589A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 31 removed outlier: 3.533A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.617A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.813A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 146 removed outlier: 7.772A pdb=" N ASP A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.134A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.178A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.178A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.834A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.022A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.644A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.765A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.202A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.253A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 20 through 31 removed outlier: 3.760A pdb=" N HIS B 66 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.672A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.817A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 141 through 146 removed outlier: 8.445A pdb=" N ASP B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.547A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.111A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.970A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.153A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.735A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.517A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.403A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 20 through 31 removed outlier: 3.527A pdb=" N THR C 20 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 68 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.669A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.357A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 144 through 146 removed outlier: 3.641A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.386A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.176A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.176A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.555A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 435 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.256A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.889A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1096 1112 hydrogen bonds defined for protein. 3042 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: 6.78 Time building geometry restraints manager: 3.59 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: 5166 1.32 - 1.45: 7390 1.45 - 1.58: 15630 1.58 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 28336 Sorted by residual: bond pdb=" N PHE A 490 " pdb=" CA PHE A 490 " ideal model delta sigma weight residual 1.457 1.542 -0.085 1.41e-02 5.03e+03 3.61e+01 bond pdb=" C PHE A 490 " pdb=" N PRO A 491 " ideal model delta sigma weight residual 1.331 1.400 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA VAL B 620 " pdb=" C VAL B 620 " ideal model delta sigma weight residual 1.520 1.562 -0.042 8.80e-03 1.29e+04 2.27e+01 bond pdb=" C5 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.413 1.508 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C5 NAG B1401 " pdb=" O5 NAG B1401 " ideal model delta sigma weight residual 1.413 1.505 -0.092 2.00e-02 2.50e+03 2.14e+01 ... (remaining 28331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 33403 2.97 - 5.94: 4881 5.94 - 8.91: 235 8.91 - 11.87: 14 11.87 - 14.84: 4 Bond angle restraints: 38537 Sorted by residual: angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 108.34 123.18 -14.84 1.64e+00 3.72e-01 8.19e+01 angle pdb=" OD1 ASN C 331 " pdb=" CG ASN C 331 " pdb=" ND2 ASN C 331 " ideal model delta sigma weight residual 122.60 113.60 9.00 1.00e+00 1.00e+00 8.09e+01 angle pdb=" C ASP A 215 " pdb=" N LEU A 216 " pdb=" CA LEU A 216 " ideal model delta sigma weight residual 122.28 129.94 -7.66 8.80e-01 1.29e+00 7.57e+01 angle pdb=" CA ASN B 709 " pdb=" CB ASN B 709 " pdb=" CG ASN B 709 " ideal model delta sigma weight residual 112.60 120.60 -8.00 1.00e+00 1.00e+00 6.40e+01 angle pdb=" N ARG A 34 " pdb=" CA ARG A 34 " pdb=" C ARG A 34 " ideal model delta sigma weight residual 110.53 120.95 -10.42 1.32e+00 5.74e-01 6.23e+01 ... (remaining 38532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14798 17.97 - 35.94: 981 35.94 - 53.91: 222 53.91 - 71.88: 65 71.88 - 89.85: 29 Dihedral angle restraints: 16095 sinusoidal: 6285 harmonic: 9810 Sorted by residual: dihedral pdb=" C CYS B 617 " pdb=" N CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta harmonic sigma weight residual -122.60 -140.64 18.04 0 2.50e+00 1.60e-01 5.21e+01 dihedral pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " ideal model delta harmonic sigma weight residual 122.80 139.82 -17.02 0 2.50e+00 1.60e-01 4.64e+01 dihedral pdb=" CA CYS B 617 " pdb=" C CYS B 617 " pdb=" N THR B 618 " pdb=" CA THR B 618 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 16092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.368: 4601 0.368 - 0.737: 24 0.737 - 1.105: 2 1.105 - 1.474: 2 1.474 - 1.842: 2 Chirality restraints: 4631 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 ... (remaining 4628 not shown) Planarity restraints: 4883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.170 2.00e-02 2.50e+03 2.06e-01 5.29e+02 pdb=" CG ASN B 709 " 0.103 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.338 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " -0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.156 2.00e-02 2.50e+03 1.84e-01 4.25e+02 pdb=" CG ASN A 709 " 0.109 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.297 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.020 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" CG ASN A 603 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.176 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.319 2.00e-02 2.50e+03 pdb=" C1 NAG A1404 " 0.186 2.00e-02 2.50e+03 ... (remaining 4880 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 22 2.25 - 2.91: 10520 2.91 - 3.58: 37530 3.58 - 4.24: 63706 4.24 - 4.90: 106777 Nonbonded interactions: 218555 Sorted by model distance: nonbonded pdb=" CG2 THR A 20 " pdb=" OD2 ASP A 80 " model vdw 1.589 3.460 nonbonded pdb=" CE1 PHE C 559 " pdb=" CG2 ILE C 584 " model vdw 1.646 3.760 nonbonded pdb=" CZ PHE C 559 " pdb=" CG2 ILE C 584 " model vdw 1.685 3.760 nonbonded pdb=" OH TYR C 453 " pdb=" CD2 LEU C 492 " model vdw 1.903 3.460 nonbonded pdb=" O MET C 900 " pdb=" CD1 TYR C 904 " model vdw 1.925 3.340 ... (remaining 218550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 624 or resid 631 through 1406)) selection = (chain 'B' and (resid 14 through 624 or resid 631 through 827 or resid 832 throu \ gh 1406)) selection = (chain 'C' and (resid 14 through 71 or resid 80 through 624 or resid 631 through \ 827 or resid 832 through 1406)) } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } 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 individual isotropic 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: 10.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.500 Find NCS groups from input model: 0.870 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.017 0.541 28481 Z= 1.013 Angle : 2.063 27.902 38924 Z= 1.316 Chirality : 0.129 1.842 4631 Planarity : 0.014 0.124 4834 Dihedral : 13.960 89.852 9658 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 1.62 % Allowed : 6.68 % Favored : 91.70 % Rotamer: Outliers : 2.22 % Allowed : 6.14 % Favored : 91.64 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.13), residues: 3339 helix: -1.90 (0.15), residues: 777 sheet: 0.10 (0.20), residues: 601 loop : -1.82 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG A 634 TYR 0.118 0.022 TYR C 449 PHE 0.114 0.016 PHE B 497 TRP 0.093 0.025 TRP B 104 HIS 0.035 0.008 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.01625 / 0.93 (28336) covalent geometry : angle 1.99751 / 1.31 (38537) SS BOND : bond 0.01542 / 1.10 ( 45) SS BOND : angle 2.64217 / 1.65 ( 90) hydrogen bonds : bond 0.17328 / 11.72 ( 1090) hydrogen bonds : angle 8.94421 / 6.20 ( 3042) Misc. bond : bond 0.52794 / 27.79 ( 1) link_ALPHA1-4 : bond 0.02641 / 1.84 ( 18) link_ALPHA1-4 : angle 3.74978 / 2.49 ( 54) link_BETA1-4 : bond 0.02470 / 1.70 ( 29) link_BETA1-4 : angle 4.18396 / 2.97 ( 87) link_BETA1-6 : bond 0.03773 / 1.89 ( 3) link_BETA1-6 : angle 2.41145 / 1.45 ( 9) link_NAG-ASN : bond 0.11981 / 4.93 ( 49) link_NAG-ASN : angle 7.81473 / 5.21 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7587 (m) REVERT: A 152 TRP cc_start: 0.8752 (m100) cc_final: 0.7783 (m100) REVERT: A 429 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7670 (t80) REVERT: A 814 LYS cc_start: 0.9118 (mttt) cc_final: 0.8852 (mmtt) REVERT: A 1029 MET cc_start: 0.9543 (tpp) cc_final: 0.9201 (tpt) REVERT: B 374 PHE cc_start: 0.7595 (p90) cc_final: 0.6898 (p90) REVERT: B 394 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8279 (p0) REVERT: B 634 ARG cc_start: 0.7289 (ttp80) cc_final: 0.6558 (ttp80) REVERT: B 988 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: C 54 LEU cc_start: 0.8884 (mt) cc_final: 0.8648 (mt) REVERT: C 104 TRP cc_start: 0.6691 (m-90) cc_final: 0.6270 (m-90) REVERT: C 117 LEU cc_start: 0.7584 (tt) cc_final: 0.7155 (mm) REVERT: C 391 CYS cc_start: -0.2473 (OUTLIER) cc_final: -0.4090 (p) outliers start: 65 outliers final: 16 residues processed: 230 average time/residue: 0.1898 time to fit residues: 68.4292 Evaluate side-chains 108 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 914 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS A 183 GLN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN B 52 GLN B 183 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 409 GLN B 448 ASN B 450 ASN B 460 ASN B 506 GLN B 519 HIS B 762 GLN B 955 ASN C 450 ASN C 762 GLN C 914 ASN C 955 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.102058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063993 restraints weight = 78995.289| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.41 r_work: 0.3003 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28481 Z= 0.159 Angle : 0.804 15.267 38924 Z= 0.392 Chirality : 0.050 0.705 4631 Planarity : 0.005 0.072 4834 Dihedral : 6.817 59.116 3663 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.52 % Favored : 95.06 % Rotamer: Outliers : 1.88 % Allowed : 8.63 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.08 (0.14), residues: 3339 helix: 0.23 (0.18), residues: 793 sheet: 0.18 (0.19), residues: 704 loop : -1.55 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.027 0.002 TYR A 160 PHE 0.031 0.002 PHE C 855 TRP 0.018 0.002 TRP A 633 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (28336) covalent geometry : angle 0.74811 / 0.38 (38537) SS BOND : bond 0.00452 / 0.29 ( 45) SS BOND : angle 1.48971 / 0.96 ( 90) hydrogen bonds : bond 0.04596 / 3.06 ( 1090) hydrogen bonds : angle 6.49259 / 4.49 ( 3042) Misc. bond : bond 0.00466 / 0.25 ( 1) link_ALPHA1-4 : bond 0.00843 / 0.64 ( 18) link_ALPHA1-4 : angle 2.44977 / 1.60 ( 54) link_BETA1-4 : bond 0.00423 / 0.24 ( 29) link_BETA1-4 : angle 1.80544 / 1.31 ( 87) link_BETA1-6 : bond 0.00823 / 0.42 ( 3) link_BETA1-6 : angle 1.49164 / 0.84 ( 9) link_NAG-ASN : bond 0.00822 / 0.55 ( 49) link_NAG-ASN : angle 4.34271 / 3.14 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 104 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 TRP cc_start: 0.8167 (m100) cc_final: 0.7959 (m100) REVERT: A 429 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7352 (t80) REVERT: A 814 LYS cc_start: 0.9173 (mttt) cc_final: 0.8837 (mmtt) REVERT: A 867 ASP cc_start: 0.8735 (m-30) cc_final: 0.8247 (p0) REVERT: B 394 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7640 (p0) REVERT: B 634 ARG cc_start: 0.7096 (ttp80) cc_final: 0.6404 (ttp80) REVERT: B 902 MET cc_start: 0.9094 (mmt) cc_final: 0.8820 (mmt) REVERT: B 988 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8459 (pm20) REVERT: C 102 ARG cc_start: 0.6675 (mmt-90) cc_final: 0.6007 (mmp-170) REVERT: C 565 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6150 (p90) outliers start: 55 outliers final: 27 residues processed: 153 average time/residue: 0.1751 time to fit residues: 43.7774 Evaluate side-chains 113 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 124 optimal weight: 0.0060 chunk 172 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 334 optimal weight: 8.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 66 HIS C 460 ASN C 519 HIS C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.100563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062311 restraints weight = 79659.524| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.40 r_work: 0.2959 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28481 Z= 0.177 Angle : 0.716 13.629 38924 Z= 0.344 Chirality : 0.047 0.544 4631 Planarity : 0.004 0.076 4834 Dihedral : 6.075 59.461 3652 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.54 % Favored : 94.10 % Rotamer: Outliers : 2.22 % Allowed : 9.08 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3339 helix: 0.83 (0.18), residues: 796 sheet: 0.23 (0.19), residues: 712 loop : -1.46 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 403 TYR 0.020 0.002 TYR C 495 PHE 0.027 0.002 PHE C 855 TRP 0.012 0.001 TRP B 633 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (28336) covalent geometry : angle 0.66781 / 0.33 (38537) SS BOND : bond 0.00341 / 0.23 ( 45) SS BOND : angle 1.21474 / 0.77 ( 90) hydrogen bonds : bond 0.04238 / 2.84 ( 1090) hydrogen bonds : angle 5.98863 / 4.14 ( 3042) Misc. bond : bond 0.00141 / 0.07 ( 1) link_ALPHA1-4 : bond 0.00845 / 0.60 ( 18) link_ALPHA1-4 : angle 1.98199 / 1.28 ( 54) link_BETA1-4 : bond 0.00284 / 0.19 ( 29) link_BETA1-4 : angle 1.42512 / 1.01 ( 87) link_BETA1-6 : bond 0.00963 / 0.48 ( 3) link_BETA1-6 : angle 1.29504 / 0.69 ( 9) link_NAG-ASN : bond 0.00702 / 0.48 ( 49) link_NAG-ASN : angle 3.91425 / 2.83 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 92 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8695 (mp) REVERT: A 177 MET cc_start: 0.8388 (ppp) cc_final: 0.7993 (ppp) REVERT: A 190 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7775 (mtp85) REVERT: A 429 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7229 (t80) REVERT: A 814 LYS cc_start: 0.9199 (mttt) cc_final: 0.8858 (mmtt) REVERT: A 867 ASP cc_start: 0.8716 (m-30) cc_final: 0.8263 (p0) REVERT: B 515 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8559 (p90) REVERT: B 634 ARG cc_start: 0.7035 (ttp80) cc_final: 0.6278 (ttp80) REVERT: B 988 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: C 102 ARG cc_start: 0.6682 (mmt180) cc_final: 0.5952 (mmp-170) REVERT: C 177 MET cc_start: 0.6745 (mpp) cc_final: 0.6538 (mpp) outliers start: 65 outliers final: 36 residues processed: 149 average time/residue: 0.1690 time to fit residues: 42.5863 Evaluate side-chains 119 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 840 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 131 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.099081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060784 restraints weight = 79555.502| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 4.36 r_work: 0.2923 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 28481 Z= 0.243 Angle : 0.721 13.726 38924 Z= 0.346 Chirality : 0.047 0.510 4631 Planarity : 0.004 0.078 4834 Dihedral : 5.863 58.068 3644 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.09 % Favored : 94.58 % Rotamer: Outliers : 2.32 % Allowed : 10.03 % Favored : 87.65 % 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: -0.80 (0.14), residues: 3339 helix: 0.89 (0.18), residues: 804 sheet: 0.16 (0.19), residues: 729 loop : -1.54 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 454 TYR 0.022 0.002 TYR C 495 PHE 0.025 0.002 PHE B 823 TRP 0.034 0.002 TRP A 152 HIS 0.009 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (28336) covalent geometry : angle 0.67560 / 0.34 (38537) SS BOND : bond 0.00387 / 0.29 ( 45) SS BOND : angle 1.26814 / 0.79 ( 90) hydrogen bonds : bond 0.04250 / 2.84 ( 1090) hydrogen bonds : angle 5.89618 / 4.07 ( 3042) Misc. bond : bond 0.00112 / 0.06 ( 1) link_ALPHA1-4 : bond 0.00738 / 0.52 ( 18) link_ALPHA1-4 : angle 1.91032 / 1.26 ( 54) link_BETA1-4 : bond 0.00321 / 0.23 ( 29) link_BETA1-4 : angle 1.42400 / 0.99 ( 87) link_BETA1-6 : bond 0.00752 / 0.37 ( 3) link_BETA1-6 : angle 1.42457 / 0.75 ( 9) link_NAG-ASN : bond 0.00729 / 0.51 ( 49) link_NAG-ASN : angle 3.78670 / 2.72 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 87 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8678 (mp) REVERT: A 177 MET cc_start: 0.8560 (ppp) cc_final: 0.7747 (ppp) REVERT: A 190 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7728 (mtp-110) REVERT: A 633 TRP cc_start: 0.8475 (OUTLIER) cc_final: 0.7722 (p-90) REVERT: A 675 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8481 (pp30) REVERT: A 814 LYS cc_start: 0.9210 (mttt) cc_final: 0.8864 (mmtt) REVERT: A 867 ASP cc_start: 0.8740 (m-30) cc_final: 0.8269 (p0) REVERT: B 515 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8544 (p90) REVERT: B 633 TRP cc_start: 0.9165 (OUTLIER) cc_final: 0.8758 (p-90) REVERT: B 634 ARG cc_start: 0.6953 (ttp80) cc_final: 0.6227 (ttp80) REVERT: B 988 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: C 351 TYR cc_start: 0.5390 (OUTLIER) cc_final: 0.5002 (p90) REVERT: C 425 LEU cc_start: -0.1898 (OUTLIER) cc_final: -0.2288 (pp) outliers start: 68 outliers final: 35 residues processed: 147 average time/residue: 0.1611 time to fit residues: 40.3951 Evaluate side-chains 125 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 315 optimal weight: 0.2980 chunk 169 optimal weight: 0.9980 chunk 157 optimal weight: 8.9990 chunk 283 optimal weight: 3.9990 chunk 330 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 268 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 87 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.099679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061655 restraints weight = 79415.612| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 4.25 r_work: 0.2946 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28481 Z= 0.171 Angle : 0.662 13.391 38924 Z= 0.316 Chirality : 0.045 0.435 4631 Planarity : 0.004 0.077 4834 Dihedral : 5.545 57.276 3640 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.91 % Favored : 94.79 % Rotamer: Outliers : 2.12 % Allowed : 10.58 % Favored : 87.30 % 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: -0.65 (0.14), residues: 3339 helix: 1.12 (0.18), residues: 802 sheet: 0.17 (0.19), residues: 717 loop : -1.45 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 158 TYR 0.021 0.001 TYR A 145 PHE 0.021 0.001 PHE B 823 TRP 0.045 0.001 TRP A 152 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (28336) covalent geometry : angle 0.61515 / 0.31 (38537) SS BOND : bond 0.00278 / 0.20 ( 45) SS BOND : angle 1.11328 / 0.67 ( 90) hydrogen bonds : bond 0.03828 / 2.56 ( 1090) hydrogen bonds : angle 5.63632 / 3.89 ( 3042) Misc. bond : bond 0.00079 / 0.04 ( 1) link_ALPHA1-4 : bond 0.00680 / 0.49 ( 18) link_ALPHA1-4 : angle 1.73825 / 1.12 ( 54) link_BETA1-4 : bond 0.00259 / 0.18 ( 29) link_BETA1-4 : angle 1.19880 / 0.84 ( 87) link_BETA1-6 : bond 0.00799 / 0.39 ( 3) link_BETA1-6 : angle 1.39705 / 0.74 ( 9) link_NAG-ASN : bond 0.00625 / 0.43 ( 49) link_NAG-ASN : angle 3.74967 / 2.66 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 92 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8684 (mp) REVERT: A 633 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.7670 (p-90) REVERT: A 675 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8497 (pp30) REVERT: A 814 LYS cc_start: 0.9185 (mttt) cc_final: 0.8853 (mmtt) REVERT: A 867 ASP cc_start: 0.8738 (m-30) cc_final: 0.8243 (p0) REVERT: B 515 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8525 (p90) REVERT: B 633 TRP cc_start: 0.9133 (OUTLIER) cc_final: 0.8733 (p-90) REVERT: B 634 ARG cc_start: 0.6885 (ttp80) cc_final: 0.6174 (ttp80) REVERT: B 830 ASP cc_start: 0.8251 (t0) cc_final: 0.7725 (t70) REVERT: B 988 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: C 351 TYR cc_start: 0.5235 (OUTLIER) cc_final: 0.4770 (p90) REVERT: C 425 LEU cc_start: -0.3103 (OUTLIER) cc_final: -0.3398 (pp) outliers start: 62 outliers final: 40 residues processed: 146 average time/residue: 0.1662 time to fit residues: 41.5240 Evaluate side-chains 133 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 215 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 251 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 677 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.099260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061458 restraints weight = 79219.440| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 4.27 r_work: 0.2933 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28481 Z= 0.187 Angle : 0.663 13.331 38924 Z= 0.316 Chirality : 0.045 0.448 4631 Planarity : 0.004 0.075 4834 Dihedral : 5.454 57.586 3640 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.70 % Favored : 95.00 % Rotamer: Outliers : 2.05 % Allowed : 11.23 % Favored : 86.72 % 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: -0.67 (0.14), residues: 3339 helix: 1.06 (0.18), residues: 813 sheet: 0.15 (0.19), residues: 723 loop : -1.45 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.020 0.001 TYR B1067 PHE 0.020 0.001 PHE B 375 TRP 0.024 0.001 TRP A 152 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (28336) covalent geometry : angle 0.61762 / 0.31 (38537) SS BOND : bond 0.00315 / 0.24 ( 45) SS BOND : angle 1.29009 / 0.85 ( 90) hydrogen bonds : bond 0.03850 / 2.59 ( 1090) hydrogen bonds : angle 5.58141 / 3.85 ( 3042) Misc. bond : bond 0.00097 / 0.05 ( 1) link_ALPHA1-4 : bond 0.00665 / 0.48 ( 18) link_ALPHA1-4 : angle 1.70291 / 1.11 ( 54) link_BETA1-4 : bond 0.00215 / 0.15 ( 29) link_BETA1-4 : angle 1.25444 / 0.86 ( 87) link_BETA1-6 : bond 0.00738 / 0.36 ( 3) link_BETA1-6 : angle 1.38981 / 0.74 ( 9) link_NAG-ASN : bond 0.00630 / 0.44 ( 49) link_NAG-ASN : angle 3.65642 / 2.60 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 92 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8678 (mp) REVERT: A 177 MET cc_start: 0.8486 (ppp) cc_final: 0.8253 (ppp) REVERT: A 633 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7811 (p-90) REVERT: A 675 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8478 (pp30) REVERT: A 814 LYS cc_start: 0.9167 (mttt) cc_final: 0.8853 (mmtt) REVERT: A 867 ASP cc_start: 0.8740 (m-30) cc_final: 0.8240 (p0) REVERT: B 515 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8609 (p90) REVERT: B 633 TRP cc_start: 0.9126 (OUTLIER) cc_final: 0.8766 (p-90) REVERT: B 634 ARG cc_start: 0.6830 (ttp80) cc_final: 0.6133 (ttp80) REVERT: B 830 ASP cc_start: 0.8240 (t0) cc_final: 0.7705 (t70) REVERT: B 988 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: C 102 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.6188 (mmp-170) REVERT: C 220 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7522 (t80) REVERT: C 351 TYR cc_start: 0.5317 (OUTLIER) cc_final: 0.4851 (p90) REVERT: C 425 LEU cc_start: -0.2368 (OUTLIER) cc_final: -0.2674 (pp) REVERT: C 830 ASP cc_start: 0.8170 (t0) cc_final: 0.7955 (t0) REVERT: C 1155 TYR cc_start: 0.4186 (OUTLIER) cc_final: 0.3843 (m-10) outliers start: 60 outliers final: 39 residues processed: 144 average time/residue: 0.1660 time to fit residues: 41.0471 Evaluate side-chains 137 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 87 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 49 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 329 optimal weight: 0.4980 chunk 240 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 370 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.099669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061986 restraints weight = 78925.365| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.23 r_work: 0.2947 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28481 Z= 0.150 Angle : 0.634 13.145 38924 Z= 0.301 Chirality : 0.044 0.432 4631 Planarity : 0.004 0.074 4834 Dihedral : 5.319 57.331 3639 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.06 % Favored : 94.64 % Rotamer: Outliers : 2.22 % Allowed : 11.37 % Favored : 86.42 % 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: -0.60 (0.14), residues: 3339 helix: 1.12 (0.18), residues: 820 sheet: 0.16 (0.19), residues: 716 loop : -1.40 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.020 0.001 TYR A1067 PHE 0.019 0.001 PHE B 338 TRP 0.024 0.001 TRP C 258 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (28336) covalent geometry : angle 0.58790 / 0.29 (38537) SS BOND : bond 0.00265 / 0.20 ( 45) SS BOND : angle 1.25342 / 0.84 ( 90) hydrogen bonds : bond 0.03651 / 2.45 ( 1090) hydrogen bonds : angle 5.48759 / 3.79 ( 3042) Misc. bond : bond 0.00075 / 0.04 ( 1) link_ALPHA1-4 : bond 0.00652 / 0.47 ( 18) link_ALPHA1-4 : angle 1.64248 / 1.06 ( 54) link_BETA1-4 : bond 0.00253 / 0.18 ( 29) link_BETA1-4 : angle 1.14495 / 0.80 ( 87) link_BETA1-6 : bond 0.00781 / 0.39 ( 3) link_BETA1-6 : angle 1.36305 / 0.74 ( 9) link_NAG-ASN : bond 0.00634 / 0.44 ( 49) link_NAG-ASN : angle 3.60960 / 2.58 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 93 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 135 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: A 633 TRP cc_start: 0.8464 (OUTLIER) cc_final: 0.7844 (p-90) REVERT: A 675 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8474 (pp30) REVERT: A 814 LYS cc_start: 0.9169 (mttt) cc_final: 0.8848 (mmtt) REVERT: A 867 ASP cc_start: 0.8714 (m-30) cc_final: 0.8222 (p0) REVERT: B 515 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8535 (p90) REVERT: B 633 TRP cc_start: 0.9120 (OUTLIER) cc_final: 0.8756 (p-90) REVERT: B 634 ARG cc_start: 0.6802 (ttp80) cc_final: 0.6109 (ttp80) REVERT: B 830 ASP cc_start: 0.8259 (t0) cc_final: 0.7772 (t70) REVERT: B 988 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: C 220 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7484 (t80) REVERT: C 351 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.4726 (p90) REVERT: C 425 LEU cc_start: -0.3074 (OUTLIER) cc_final: -0.3313 (pp) REVERT: C 633 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.8040 (p-90) REVERT: C 830 ASP cc_start: 0.8150 (t0) cc_final: 0.7932 (t0) REVERT: C 1155 TYR cc_start: 0.4178 (OUTLIER) cc_final: 0.3819 (m-10) outliers start: 65 outliers final: 42 residues processed: 148 average time/residue: 0.1554 time to fit residues: 38.7916 Evaluate side-chains 140 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 86 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 236 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 273 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 99 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.098445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060272 restraints weight = 79430.452| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 4.24 r_work: 0.2914 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 28481 Z= 0.237 Angle : 0.683 13.485 38924 Z= 0.326 Chirality : 0.046 0.465 4631 Planarity : 0.004 0.072 4834 Dihedral : 5.428 58.708 3639 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.60 % Favored : 94.10 % Rotamer: Outliers : 2.05 % Allowed : 11.67 % Favored : 86.28 % 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: -0.66 (0.14), residues: 3339 helix: 1.06 (0.18), residues: 807 sheet: 0.19 (0.19), residues: 704 loop : -1.43 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1107 TYR 0.034 0.002 TYR C 904 PHE 0.020 0.002 PHE B 375 TRP 0.020 0.001 TRP A 152 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (28336) covalent geometry : angle 0.63892 / 0.32 (38537) SS BOND : bond 0.00351 / 0.26 ( 45) SS BOND : angle 1.26806 / 0.81 ( 90) hydrogen bonds : bond 0.04029 / 2.68 ( 1090) hydrogen bonds : angle 5.61787 / 3.87 ( 3042) Misc. bond : bond 0.00112 / 0.06 ( 1) link_ALPHA1-4 : bond 0.00673 / 0.49 ( 18) link_ALPHA1-4 : angle 1.66848 / 1.08 ( 54) link_BETA1-4 : bond 0.00198 / 0.14 ( 29) link_BETA1-4 : angle 1.32321 / 0.90 ( 87) link_BETA1-6 : bond 0.00686 / 0.34 ( 3) link_BETA1-6 : angle 1.37667 / 0.76 ( 9) link_NAG-ASN : bond 0.00652 / 0.45 ( 49) link_NAG-ASN : angle 3.64526 / 2.59 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 86 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8567 (mp) REVERT: A 135 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.6006 (m-80) REVERT: A 633 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.7667 (p-90) REVERT: A 636 TYR cc_start: 0.6949 (m-80) cc_final: 0.6611 (m-80) REVERT: A 675 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8417 (pp30) REVERT: A 814 LYS cc_start: 0.9195 (mttt) cc_final: 0.8892 (mmtt) REVERT: A 867 ASP cc_start: 0.8755 (m-30) cc_final: 0.8293 (p0) REVERT: B 515 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8665 (p90) REVERT: B 633 TRP cc_start: 0.9125 (OUTLIER) cc_final: 0.8728 (p-90) REVERT: B 634 ARG cc_start: 0.6811 (ttp80) cc_final: 0.6132 (ttp80) REVERT: B 830 ASP cc_start: 0.8283 (t0) cc_final: 0.7792 (t70) REVERT: B 988 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: C 220 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7545 (t80) REVERT: C 351 TYR cc_start: 0.5251 (OUTLIER) cc_final: 0.4753 (p90) REVERT: C 425 LEU cc_start: -0.2958 (OUTLIER) cc_final: -0.3190 (pp) REVERT: C 633 TRP cc_start: 0.8574 (OUTLIER) cc_final: 0.7994 (p-90) REVERT: C 1155 TYR cc_start: 0.4074 (OUTLIER) cc_final: 0.3707 (m-10) outliers start: 60 outliers final: 40 residues processed: 136 average time/residue: 0.1655 time to fit residues: 38.5120 Evaluate side-chains 132 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 80 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 42 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 257 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 326 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 321 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.099291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062265 restraints weight = 79651.048| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.74 r_work: 0.2992 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28481 Z= 0.185 Angle : 0.648 13.304 38924 Z= 0.308 Chirality : 0.045 0.429 4631 Planarity : 0.004 0.071 4834 Dihedral : 5.338 58.823 3639 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.76 % Favored : 94.94 % Rotamer: Outliers : 2.01 % Allowed : 11.91 % Favored : 86.08 % 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: -0.60 (0.14), residues: 3339 helix: 1.16 (0.18), residues: 812 sheet: 0.14 (0.19), residues: 721 loop : -1.41 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 493 TYR 0.019 0.001 TYR B1067 PHE 0.023 0.001 PHE B 374 TRP 0.016 0.001 TRP A 152 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (28336) covalent geometry : angle 0.60435 / 0.30 (38537) SS BOND : bond 0.00289 / 0.22 ( 45) SS BOND : angle 1.15020 / 0.74 ( 90) hydrogen bonds : bond 0.03746 / 2.50 ( 1090) hydrogen bonds : angle 5.49379 / 3.78 ( 3042) Misc. bond : bond 0.00078 / 0.04 ( 1) link_ALPHA1-4 : bond 0.00633 / 0.46 ( 18) link_ALPHA1-4 : angle 1.59876 / 1.04 ( 54) link_BETA1-4 : bond 0.00228 / 0.17 ( 29) link_BETA1-4 : angle 1.16870 / 0.81 ( 87) link_BETA1-6 : bond 0.00687 / 0.34 ( 3) link_BETA1-6 : angle 1.34526 / 0.77 ( 9) link_NAG-ASN : bond 0.00611 / 0.42 ( 49) link_NAG-ASN : angle 3.57199 / 2.55 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 84 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 135 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.5935 (m-80) REVERT: A 429 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7270 (t80) REVERT: A 633 TRP cc_start: 0.8586 (OUTLIER) cc_final: 0.7711 (p-90) REVERT: A 636 TYR cc_start: 0.6845 (m-80) cc_final: 0.6598 (m-80) REVERT: A 867 ASP cc_start: 0.8719 (m-30) cc_final: 0.8399 (p0) REVERT: B 515 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8702 (p90) REVERT: B 519 HIS cc_start: 0.8614 (m-70) cc_final: 0.8393 (m-70) REVERT: B 633 TRP cc_start: 0.9098 (OUTLIER) cc_final: 0.8635 (p-90) REVERT: B 634 ARG cc_start: 0.6836 (ttp80) cc_final: 0.6190 (ttp80) REVERT: B 830 ASP cc_start: 0.8117 (t0) cc_final: 0.7730 (t70) REVERT: C 102 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6467 (mmp-170) REVERT: C 220 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7776 (t80) REVERT: C 351 TYR cc_start: 0.5100 (OUTLIER) cc_final: 0.4407 (p90) REVERT: C 633 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.7837 (p-90) REVERT: C 1155 TYR cc_start: 0.3952 (OUTLIER) cc_final: 0.3539 (m-10) outliers start: 59 outliers final: 39 residues processed: 134 average time/residue: 0.1643 time to fit residues: 37.7054 Evaluate side-chains 130 residues out of total 2930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 80 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 633 TRP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1155 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6331 > 50: distance: 33 - 155: 36.446 distance: 50 - 132: 27.234 distance: 62 - 117: 30.896 distance: 65 - 114: 35.222 distance: 103 - 107: 29.112 distance: 107 - 108: 24.233 distance: 108 - 109: 24.001 distance: 108 - 111: 28.466 distance: 109 - 110: 44.421 distance: 109 - 114: 40.543 distance: 111 - 113: 13.653 distance: 114 - 115: 6.356 distance: 115 - 116: 7.762 distance: 115 - 118: 19.302 distance: 116 - 125: 38.700 distance: 118 - 119: 9.486 distance: 119 - 120: 6.099 distance: 119 - 121: 5.961 distance: 120 - 122: 10.185 distance: 121 - 123: 26.370 distance: 122 - 124: 24.840 distance: 123 - 124: 13.609 distance: 125 - 126: 41.030 distance: 126 - 127: 21.183 distance: 126 - 129: 17.431 distance: 127 - 128: 42.540 distance: 127 - 132: 25.140 distance: 129 - 130: 3.264 distance: 129 - 131: 25.594 distance: 132 - 133: 20.019 distance: 133 - 134: 42.197 distance: 133 - 136: 38.075 distance: 134 - 135: 35.662 distance: 134 - 138: 14.870 distance: 136 - 137: 40.099 distance: 138 - 139: 26.952 distance: 139 - 140: 31.483 distance: 140 - 141: 10.057 distance: 140 - 142: 12.845 distance: 142 - 143: 37.464 distance: 143 - 144: 54.007 distance: 143 - 146: 27.545 distance: 144 - 145: 40.109 distance: 144 - 150: 33.668 distance: 146 - 147: 35.382 distance: 147 - 148: 10.599 distance: 147 - 149: 30.793 distance: 150 - 151: 8.980 distance: 151 - 154: 40.015 distance: 154 - 155: 36.087 distance: 156 - 157: 27.910 distance: 157 - 158: 30.002 distance: 157 - 160: 19.843 distance: 158 - 159: 30.962 distance: 158 - 164: 20.171 distance: 160 - 161: 32.962 distance: 161 - 162: 32.382 distance: 161 - 163: 20.056 distance: 164 - 165: 31.681 distance: 165 - 168: 15.550 distance: 166 - 167: 39.984 distance: 166 - 171: 7.496 distance: 172 - 173: 38.863 distance: 172 - 175: 29.093 distance: 173 - 174: 13.901 distance: 173 - 178: 28.343 distance: 175 - 176: 17.689 distance: 175 - 177: 32.820