Starting phenix.real_space_refine on Fri Jun 27 21:52:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzh_27798/06_2025/8dzh_27798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzh_27798/06_2025/8dzh_27798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dzh_27798/06_2025/8dzh_27798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzh_27798/06_2025/8dzh_27798.map" model { file = "/net/cci-nas-00/data/ceres_data/8dzh_27798/06_2025/8dzh_27798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzh_27798/06_2025/8dzh_27798.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 140 5.16 5 C 20324 2.51 5 N 5235 2.21 5 O 6257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31956 Number of models: 1 Model: "" Number of chains: 39 Chain: "B" Number of atoms: 8562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8562 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 60, 'TRANS': 1031} Chain breaks: 5 Chain: "A" Number of atoms: 8606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8606 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 60, 'TRANS': 1039} Chain breaks: 7 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 8561 Classifications: {'peptide': 1093} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 60, 'TRANS': 1032} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "I" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 25.09, per 1000 atoms: 0.79 Number of scatterers: 31956 At special positions: 0 Unit cell: (145.52, 148.73, 218.28, 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 140 16.00 O 6257 8.00 N 5235 7.00 C 20324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.04 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 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 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1301 " - " ASN A 231 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 613 " " NAG A1305 " - " ASN A 654 " " NAG B1301 " - " ASN B 613 " " NAG B1302 " - " ASN B 328 " " NAG B1303 " - " ASN B 654 " " NAG B1304 " - " ASN B1071 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 123 " " NAG B1307 " - " ASN B 231 " " NAG C1301 " - " ASN C 600 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 613 " " NAG C1304 " - " ASN C 654 " " NAG C1305 " - " ASN C 160 " " NAG C1306 " - " ASN C 120 " " NAG F 1 " - " ASN B 340 " " NAG G 1 " - " ASN B 798 " " NAG K 1 " - " ASN B 714 " " NAG M 1 " - " ASN B 706 " " NAG N 1 " - " ASN B1131 " " NAG O 1 " - " ASN B1095 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN A1071 " " NAG R 1 " - " ASN A 340 " " NAG S 1 " - " ASN A 120 " " NAG T 1 " - " ASN A 135 " " NAG U 1 " - " ASN A 279 " " NAG V 1 " - " ASN A 706 " " NAG W 1 " - " ASN A1131 " " NAG X 1 " - " ASN A1095 " " NAG Y 1 " - " ASN A 714 " " NAG Z 1 " - " ASN A 798 " " NAG a 1 " - " ASN C 328 " " NAG b 1 " - " ASN C1095 " " NAG c 1 " - " ASN C1131 " " NAG d 1 " - " ASN C 706 " " NAG e 1 " - " ASN C 714 " " NAG f 1 " - " ASN C 798 " " NAG g 1 " - " ASN C1071 " " NAG h 1 " - " ASN C 279 " " NAG i 1 " - " ASN C 231 " " NAG j 1 " - " ASN C 340 " Time building additional restraints: 9.78 Conformation dependent library (CDL) restraints added in 4.4 seconds 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7360 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 58 sheets defined 21.2% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.95 Creating SS restraints... Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.841A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.729A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.942A pdb=" N ASN B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 4.124A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 497 through 501 removed outlier: 3.738A pdb=" N GLY B 501 " --> pdb=" O TYR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.981A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 825 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.148A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 937 removed outlier: 3.610A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 965 removed outlier: 3.502A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.190A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B1015 " --> pdb=" O ARG B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1142 removed outlier: 3.902A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.753A pdb=" N VAL A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.576A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.569A pdb=" N ASN A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.781A pdb=" N GLN A 503 " --> pdb=" O GLY A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.514A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.609A pdb=" N GLN A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 846 through 852 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.561A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.156A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.559A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 964 removed outlier: 4.156A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.350A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1142 removed outlier: 4.473A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1137 through 1142' Processing helix chain 'C' and resid 70 through 73 No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.832A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.858A pdb=" N LEU C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.267A pdb=" N ASN C 385 " --> pdb=" O PRO C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.650A pdb=" N SER C 440 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 754 removed outlier: 3.510A pdb=" N GLY C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 Processing helix chain 'C' and resid 813 through 824 Processing helix chain 'C' and resid 846 through 853 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.708A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.245A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.584A pdb=" N PHE C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.037A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1142 removed outlier: 3.949A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.887A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.846A pdb=" N THR B 63 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 184 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N HIS B 202 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N LEU B 220 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.298A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.816A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 83 Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.849A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA B 240 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE B 99 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 126 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE B 163 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL B 128 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N CYS B 161 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.686A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.106A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.957A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS B 429 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.915A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.963A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AB3, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.644A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.644A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.397A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 784 through 787 removed outlier: 5.798A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.236A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.549A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 63 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 50 through 55 removed outlier: 4.041A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AC2, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.141A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA A 240 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE A 99 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 126 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 164 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 128 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASN A 160 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.500A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 322 through 325 removed outlier: 5.705A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.808A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 373 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AC7, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AC8, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.972A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 698 through 700 removed outlier: 6.520A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 708 through 725 removed outlier: 7.014A pdb=" N GLN A1068 " --> pdb=" O THR A 713 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE A 715 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 717 " --> pdb=" O TYR A1064 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR A1064 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 719 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A1062 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 721 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A1060 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 723 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A1058 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY A1056 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 708 through 725 removed outlier: 7.014A pdb=" N GLN A1068 " --> pdb=" O THR A 713 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE A 715 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 717 " --> pdb=" O TYR A1064 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR A1064 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 719 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A1062 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A 721 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A1060 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 723 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A1058 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY A1056 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.334A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.393A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.309A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.017A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.525A pdb=" N LEU C 238 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 126 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE C 163 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL C 128 " --> pdb=" O CYS C 161 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N CYS C 161 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 316 removed outlier: 7.001A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.660A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 507 " --> pdb=" O PHE C 397 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 432 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.200A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 450 through 451 Processing sheet with id=AE3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE4, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.806A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.796A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.796A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.526A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AE9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.834A pdb=" N ILE E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.715A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.715A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 98 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.592A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.499A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.365A pdb=" N GLU I 10 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP I 33 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AG4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.978A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3246 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: 17.28 Time building geometry restraints manager: 11.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.18: 4 1.18 - 1.41: 13373 1.41 - 1.64: 19136 1.64 - 1.88: 181 1.88 - 2.11: 4 Bond restraints: 32698 Sorted by residual: bond pdb=" CD1 PHE C 830 " pdb=" CE1 PHE C 830 " ideal model delta sigma weight residual 1.382 2.106 -0.724 3.00e-02 1.11e+03 5.82e+02 bond pdb=" CD2 PHE C 830 " pdb=" CE2 PHE C 830 " ideal model delta sigma weight residual 1.382 2.104 -0.722 3.00e-02 1.11e+03 5.79e+02 bond pdb=" CD2 TYR B 450 " pdb=" CE2 TYR B 450 " ideal model delta sigma weight residual 1.382 2.064 -0.682 3.00e-02 1.11e+03 5.16e+02 bond pdb=" CD1 TYR B 450 " pdb=" CE1 TYR B 450 " ideal model delta sigma weight residual 1.382 2.063 -0.681 3.00e-02 1.11e+03 5.16e+02 bond pdb=" CE2 PHE C 830 " pdb=" CZ PHE C 830 " ideal model delta sigma weight residual 1.382 0.951 0.431 3.00e-02 1.11e+03 2.06e+02 ... (remaining 32693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.83: 44440 14.83 - 29.67: 10 29.67 - 44.50: 2 44.50 - 59.34: 1 59.34 - 74.17: 1 Bond angle restraints: 44454 Sorted by residual: angle pdb=" CE1 TYR B 450 " pdb=" CZ TYR B 450 " pdb=" CE2 TYR B 450 " ideal model delta sigma weight residual 120.30 46.13 74.17 2.00e+00 2.50e-01 1.38e+03 angle pdb=" CE1 PHE C 830 " pdb=" CZ PHE C 830 " pdb=" CE2 PHE C 830 " ideal model delta sigma weight residual 120.00 68.46 51.54 1.80e+00 3.09e-01 8.20e+02 angle pdb=" CD1 PHE C 830 " pdb=" CG PHE C 830 " pdb=" CD2 PHE C 830 " ideal model delta sigma weight residual 118.60 88.11 30.49 1.50e+00 4.44e-01 4.13e+02 angle pdb=" CD1 TYR B 450 " pdb=" CG TYR B 450 " pdb=" CD2 TYR B 450 " ideal model delta sigma weight residual 118.10 87.79 30.31 1.50e+00 4.44e-01 4.08e+02 angle pdb=" CG TYR B 450 " pdb=" CD1 TYR B 450 " pdb=" CE1 TYR B 450 " ideal model delta sigma weight residual 121.20 97.10 24.10 1.50e+00 4.44e-01 2.58e+02 ... (remaining 44449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.86: 18229 24.86 - 49.73: 1680 49.73 - 74.59: 295 74.59 - 99.46: 144 99.46 - 124.32: 80 Dihedral angle restraints: 20428 sinusoidal: 8943 harmonic: 11485 Sorted by residual: dihedral pdb=" CB CYS C 837 " pdb=" SG CYS C 837 " pdb=" SG CYS C 848 " pdb=" CB CYS C 848 " ideal model delta sinusoidal sigma weight residual 93.00 179.28 -86.28 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS A 837 " pdb=" SG CYS A 837 " pdb=" SG CYS A 848 " pdb=" CB CYS A 848 " ideal model delta sinusoidal sigma weight residual 93.00 167.87 -74.87 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CA VAL A 612 " pdb=" C VAL A 612 " pdb=" N ASN A 613 " pdb=" CA ASN A 613 " ideal model delta harmonic sigma weight residual 180.00 138.80 41.20 0 5.00e+00 4.00e-02 6.79e+01 ... (remaining 20425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 5153 0.302 - 0.605: 7 0.605 - 0.907: 5 0.907 - 1.210: 0 1.210 - 1.512: 2 Chirality restraints: 5167 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.72e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 798 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.09 -1.31 2.00e-01 2.50e+01 4.27e+01 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 714 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 5164 not shown) Planarity restraints: 5694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 613 " 0.086 2.00e-02 2.50e+03 8.35e-02 8.71e+01 pdb=" CG ASN A 613 " -0.107 2.00e-02 2.50e+03 pdb=" OD1 ASN A 613 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 613 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 798 " -0.089 2.00e-02 2.50e+03 8.14e-02 8.27e+01 pdb=" CG ASN B 798 " 0.100 2.00e-02 2.50e+03 pdb=" OD1 ASN B 798 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 798 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 422 " -0.094 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO B 423 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " -0.081 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " -0.071 5.00e-02 4.00e+02 ... (remaining 5691 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 60 2.29 - 2.94: 16415 2.94 - 3.60: 50880 3.60 - 4.25: 80515 4.25 - 4.90: 127425 Nonbonded interactions: 275295 Sorted by model distance: nonbonded pdb=" CD2 PHE C 830 " pdb=" CE1 PHE C 830 " model vdw 1.642 2.912 nonbonded pdb=" CD2 TYR B 450 " pdb=" CE1 TYR B 450 " model vdw 1.644 2.912 nonbonded pdb=" CD1 PHE C 830 " pdb=" CE2 PHE C 830 " model vdw 1.644 2.912 nonbonded pdb=" CD1 TYR B 450 " pdb=" CE2 TYR B 450 " model vdw 1.646 2.912 nonbonded pdb=" OH TYR C 348 " pdb=" O ILE C 465 " model vdw 2.097 3.040 ... (remaining 275290 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 19 through 145 or resid 149 through 621 or resid 625 throu \ gh 837 or resid 848 through 1144 or resid 1301 through 1306)) selection = (chain 'B' and (resid 19 through 145 or resid 149 through 441 or resid 444 throu \ gh 1144 or resid 1301 through 1306)) selection = (chain 'C' and (resid 19 through 837 or resid 848 through 1144 or resid 1301 thr \ ough 1306)) } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.830 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: 0.060 Extract box with map and model: 1.460 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 88.790 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.360 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: 0.020 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.010 0.724 32818 Z= 0.382 Angle : 0.973 74.169 44766 Z= 0.492 Chirality : 0.059 1.512 5167 Planarity : 0.005 0.142 5649 Dihedral : 21.507 124.320 12924 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.32 % Favored : 94.48 % Rotamer: Outliers : 0.26 % Allowed : 30.13 % Favored : 69.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3913 helix: 2.85 (0.20), residues: 666 sheet: -0.28 (0.17), residues: 926 loop : -0.78 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 433 HIS 0.006 0.001 HIS C 202 PHE 0.030 0.001 PHE I 29 TYR 0.038 0.001 TYR B 450 ARG 0.004 0.000 ARG C 506 Details of bonding type rmsd link_NAG-ASN : bond 0.01173 ( 45) link_NAG-ASN : angle 6.54886 ( 135) link_BETA1-4 : bond 0.00764 ( 27) link_BETA1-4 : angle 2.87981 ( 81) hydrogen bonds : bond 0.21795 ( 1151) hydrogen bonds : angle 8.72587 ( 3246) SS BOND : bond 0.00282 ( 48) SS BOND : angle 0.95984 ( 96) covalent geometry : bond 0.01005 (32698) covalent geometry : angle 0.89728 (44454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 959 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9374 (mt) REVERT: E 40 MET cc_start: 0.9410 (mmm) cc_final: 0.9155 (mmm) outliers start: 9 outliers final: 4 residues processed: 57 average time/residue: 0.4219 time to fit residues: 44.3292 Evaluate side-chains 51 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 158 optimal weight: 30.0000 chunk 306 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 228 optimal weight: 20.0000 chunk 355 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN B 406 GLN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 478 ASN B 625 GLN B 781 GLN B 910 GLN B 923 GLN B 952 ASN B 954 GLN B 989 GLN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN A 471 GLN A 625 GLN A 752 GLN A 801 GLN A 869 GLN A 910 GLN A 932 GLN A 952 ASN A1002 GLN A1008 GLN C 484 ASN C 625 GLN C 638 ASN C 687 GLN C 850 GLN ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.026715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.019659 restraints weight = 475160.100| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 5.25 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.724 32818 Z= 0.389 Angle : 0.964 74.111 44766 Z= 0.487 Chirality : 0.052 0.988 5167 Planarity : 0.006 0.141 5649 Dihedral : 16.328 112.358 5817 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.14 % Favored : 94.66 % Rotamer: Outliers : 3.47 % Allowed : 27.53 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 3913 helix: 2.35 (0.19), residues: 709 sheet: -0.40 (0.17), residues: 946 loop : -0.78 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 433 HIS 0.006 0.001 HIS C 202 PHE 0.021 0.001 PHE I 29 TYR 0.041 0.002 TYR B 450 ARG 0.004 0.001 ARG A 506 Details of bonding type rmsd link_NAG-ASN : bond 0.00813 ( 45) link_NAG-ASN : angle 4.90111 ( 135) link_BETA1-4 : bond 0.00589 ( 27) link_BETA1-4 : angle 2.59235 ( 81) hydrogen bonds : bond 0.05189 ( 1151) hydrogen bonds : angle 6.69384 ( 3246) SS BOND : bond 0.00342 ( 48) SS BOND : angle 1.00801 ( 96) covalent geometry : bond 0.01023 (32698) covalent geometry : angle 0.92157 (44454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 47 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 398 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8320 (m) REVERT: C 172 MET cc_start: 0.8936 (mmm) cc_final: 0.8636 (mmm) REVERT: C 436 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7861 (m-40) REVERT: C 730 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8550 (mtmm) REVERT: C 834 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8439 (p90) REVERT: H 105 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7467 (p90) REVERT: L 1 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8428 (pt0) REVERT: L 21 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9192 (tp) REVERT: L 78 ARG cc_start: 0.9646 (mmm-85) cc_final: 0.9430 (mmm-85) REVERT: L 80 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.8901 (mm-30) outliers start: 119 outliers final: 59 residues processed: 162 average time/residue: 0.4068 time to fit residues: 113.7307 Evaluate side-chains 113 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 46 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 348 TYR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 834 TYR Chi-restraints excluded: chain C residue 837 CYS Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 118 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 286 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 302 optimal weight: 0.0050 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 850 GLN C 502 HIS C 759 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.026774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.019738 restraints weight = 477871.989| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 5.27 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.724 32818 Z= 0.348 Angle : 0.913 74.133 44766 Z= 0.462 Chirality : 0.049 0.796 5167 Planarity : 0.005 0.139 5649 Dihedral : 14.034 111.366 5813 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 3.82 % Allowed : 27.21 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.13), residues: 3913 helix: 2.49 (0.19), residues: 693 sheet: -0.30 (0.17), residues: 920 loop : -0.82 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 433 HIS 0.005 0.001 HIS C 66 PHE 0.017 0.001 PHE C 65 TYR 0.040 0.001 TYR B 450 ARG 0.010 0.001 ARG C 495 Details of bonding type rmsd link_NAG-ASN : bond 0.00647 ( 45) link_NAG-ASN : angle 4.54426 ( 135) link_BETA1-4 : bond 0.00635 ( 27) link_BETA1-4 : angle 2.80572 ( 81) hydrogen bonds : bond 0.04573 ( 1151) hydrogen bonds : angle 6.26505 ( 3246) SS BOND : bond 0.00249 ( 48) SS BOND : angle 0.85825 ( 96) covalent geometry : bond 0.00957 (32698) covalent geometry : angle 0.87257 (44454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 46 time to evaluate : 4.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 398 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8286 (m) REVERT: B 613 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8042 (m-40) REVERT: A 694 MET cc_start: 0.8599 (ptm) cc_final: 0.8382 (ptm) REVERT: C 436 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7874 (m-40) REVERT: C 730 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8646 (mtmm) REVERT: C 834 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8271 (p90) REVERT: C 850 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.8946 (mm-40) REVERT: H 105 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7371 (p90) REVERT: L 1 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8530 (pt0) REVERT: L 6 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7010 (mt0) REVERT: L 47 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7593 (mt) outliers start: 131 outliers final: 73 residues processed: 174 average time/residue: 0.4705 time to fit residues: 148.2134 Evaluate side-chains 129 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 46 time to evaluate : 6.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 613 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 833 GLN Chi-restraints excluded: chain C residue 834 TYR Chi-restraints excluded: chain C residue 837 CYS Chi-restraints excluded: chain C residue 850 GLN Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 7.9990 chunk 229 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 0 optimal weight: 80.0000 chunk 305 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 193 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 362 optimal weight: 8.9990 overall best weight: 6.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 975 ASN C 434 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.026521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.019438 restraints weight = 477304.892| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 5.26 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.724 32818 Z= 0.395 Angle : 0.930 74.114 44766 Z= 0.472 Chirality : 0.049 0.717 5167 Planarity : 0.005 0.138 5649 Dihedral : 12.879 111.324 5811 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.42 % Favored : 94.38 % Rotamer: Outliers : 4.81 % Allowed : 26.66 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 3913 helix: 2.35 (0.19), residues: 700 sheet: -0.42 (0.16), residues: 996 loop : -0.83 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 433 HIS 0.006 0.001 HIS C 202 PHE 0.017 0.001 PHE C 830 TYR 0.036 0.002 TYR B 450 ARG 0.005 0.001 ARG A 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00763 ( 45) link_NAG-ASN : angle 4.24292 ( 135) link_BETA1-4 : bond 0.00564 ( 27) link_BETA1-4 : angle 2.74517 ( 81) hydrogen bonds : bond 0.04388 ( 1151) hydrogen bonds : angle 6.19397 ( 3246) SS BOND : bond 0.00329 ( 48) SS BOND : angle 1.00083 ( 96) covalent geometry : bond 0.01034 (32698) covalent geometry : angle 0.89434 (44454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 47 time to evaluate : 3.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 398 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8238 (m) REVERT: B 613 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8041 (m-40) REVERT: A 897 MET cc_start: 0.8615 (mtp) cc_final: 0.8223 (mtt) REVERT: C 190 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8916 (ptmt) REVERT: C 730 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.8900 (mtmm) REVERT: C 834 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8222 (p90) REVERT: H 105 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7374 (p90) REVERT: L 6 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7320 (mt0) REVERT: L 47 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.7707 (mt) REVERT: L 80 GLU cc_start: 0.9511 (OUTLIER) cc_final: 0.9164 (mm-30) outliers start: 165 outliers final: 109 residues processed: 209 average time/residue: 0.3907 time to fit residues: 140.7880 Evaluate side-chains 164 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 46 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 613 ASN Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 348 TYR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 503 GLN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 834 TYR Chi-restraints excluded: chain C residue 837 CYS Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 83 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 308 optimal weight: 7.9990 chunk 333 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 378 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 344 optimal weight: 30.0000 chunk 217 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.026541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.019569 restraints weight = 476760.972| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 5.04 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.724 32818 Z= 0.379 Angle : 0.918 74.103 44766 Z= 0.465 Chirality : 0.049 0.672 5167 Planarity : 0.005 0.136 5649 Dihedral : 12.441 111.420 5811 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.16 % Favored : 94.63 % Rotamer: Outliers : 5.22 % Allowed : 26.51 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 3913 helix: 2.38 (0.19), residues: 700 sheet: -0.42 (0.16), residues: 979 loop : -0.82 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 433 HIS 0.008 0.001 HIS A 66 PHE 0.014 0.001 PHE C 65 TYR 0.033 0.001 TYR B 450 ARG 0.009 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 45) link_NAG-ASN : angle 4.16635 ( 135) link_BETA1-4 : bond 0.00589 ( 27) link_BETA1-4 : angle 2.78844 ( 81) hydrogen bonds : bond 0.04239 ( 1151) hydrogen bonds : angle 6.11302 ( 3246) SS BOND : bond 0.00325 ( 48) SS BOND : angle 1.19856 ( 96) covalent geometry : bond 0.01006 (32698) covalent geometry : angle 0.88244 (44454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 46 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.7911 (m-90) REVERT: B 398 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8161 (m) REVERT: B 613 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8053 (m-40) REVERT: A 897 MET cc_start: 0.8595 (mtp) cc_final: 0.8200 (mtt) REVERT: A 910 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: C 159 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8696 (p0) REVERT: C 730 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.8655 (mtmm) REVERT: C 834 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8196 (p90) REVERT: C 850 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.8974 (mm-40) REVERT: H 105 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7306 (p90) REVERT: L 6 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7288 (mt0) REVERT: L 47 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.7653 (mt) REVERT: L 80 GLU cc_start: 0.9504 (OUTLIER) cc_final: 0.9155 (mm-30) outliers start: 179 outliers final: 127 residues processed: 220 average time/residue: 0.3709 time to fit residues: 141.9923 Evaluate side-chains 185 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 46 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 288 CYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 613 ASN Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 910 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 348 TYR Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 503 GLN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 834 TYR Chi-restraints excluded: chain C residue 837 CYS Chi-restraints excluded: chain C residue 850 GLN Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 329 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 319 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 386 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN C 561 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.026516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.019554 restraints weight = 473055.046| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 5.04 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.724 32818 Z= 0.357 Angle : 0.904 74.131 44766 Z= 0.458 Chirality : 0.048 0.630 5167 Planarity : 0.005 0.134 5649 Dihedral : 11.939 111.130 5811 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.44 % Favored : 94.38 % Rotamer: Outliers : 5.07 % Allowed : 26.57 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 3913 helix: 2.43 (0.19), residues: 698 sheet: -0.45 (0.17), residues: 957 loop : -0.82 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 433 HIS 0.005 0.001 HIS C 202 PHE 0.015 0.001 PHE C 65 TYR 0.033 0.001 TYR C 492 ARG 0.006 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 45) link_NAG-ASN : angle 4.07859 ( 135) link_BETA1-4 : bond 0.00629 ( 27) link_BETA1-4 : angle 2.84585 ( 81) hydrogen bonds : bond 0.04050 ( 1151) hydrogen bonds : angle 6.00066 ( 3246) SS BOND : bond 0.00271 ( 48) SS BOND : angle 1.20956 ( 96) covalent geometry : bond 0.00972 (32698) covalent geometry : angle 0.86822 (44454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 46 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.7890 (m-90) REVERT: B 398 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8114 (m) REVERT: B 613 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8048 (m-40) REVERT: A 897 MET cc_start: 0.8626 (mtp) cc_final: 0.8245 (mtt) REVERT: A 910 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8494 (pm20) REVERT: C 159 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.8747 (p0) REVERT: C 190 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8846 (ptmt) REVERT: C 202 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.7146 (t70) REVERT: C 350 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.8070 (p-90) REVERT: C 469 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8343 (pt) REVERT: C 730 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.8675 (mtmm) REVERT: C 834 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8141 (p90) REVERT: E 40 MET cc_start: 0.9310 (mmm) cc_final: 0.9105 (mmm) REVERT: D 46 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8682 (tmm-80) REVERT: H 105 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7405 (p90) REVERT: L 6 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7285 (mt0) REVERT: L 47 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.7751 (mt) outliers start: 174 outliers final: 135 residues processed: 212 average time/residue: 0.3919 time to fit residues: 142.9847 Evaluate side-chains 196 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 46 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 613 ASN Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 910 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 348 TYR Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 503 GLN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 834 TYR Chi-restraints excluded: chain C residue 837 CYS Chi-restraints excluded: chain C residue 850 GLN Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 66 optimal weight: 9.9990 chunk 363 optimal weight: 40.0000 chunk 59 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 380 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 238 optimal weight: 20.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN C 801 GLN ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.026406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.019378 restraints weight = 479253.502| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 5.20 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.724 32818 Z= 0.399 Angle : 0.925 74.108 44766 Z= 0.470 Chirality : 0.048 0.603 5167 Planarity : 0.005 0.134 5649 Dihedral : 11.636 110.916 5811 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.55 % Favored : 94.28 % Rotamer: Outliers : 5.37 % Allowed : 26.42 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 3913 helix: 2.38 (0.19), residues: 699 sheet: -0.47 (0.16), residues: 988 loop : -0.81 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 433 HIS 0.006 0.001 HIS C 202 PHE 0.016 0.001 PHE C 65 TYR 0.029 0.002 TYR B 450 ARG 0.005 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 45) link_NAG-ASN : angle 4.14473 ( 135) link_BETA1-4 : bond 0.00564 ( 27) link_BETA1-4 : angle 2.84336 ( 81) hydrogen bonds : bond 0.04208 ( 1151) hydrogen bonds : angle 6.05891 ( 3246) SS BOND : bond 0.00330 ( 48) SS BOND : angle 1.21521 ( 96) covalent geometry : bond 0.01041 (32698) covalent geometry : angle 0.89006 (44454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 46 time to evaluate : 3.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.7982 (m-90) REVERT: B 398 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8186 (m) REVERT: B 613 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8086 (m-40) REVERT: A 831 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7304 (mp) REVERT: A 897 MET cc_start: 0.9060 (mtp) cc_final: 0.8716 (mtt) REVERT: A 910 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8582 (pm20) REVERT: C 159 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8759 (p0) REVERT: C 190 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8823 (ptmt) REVERT: C 350 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.7994 (p-90) REVERT: C 436 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7666 (m-40) REVERT: C 469 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8303 (pt) REVERT: C 730 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8692 (mtmm) REVERT: C 834 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8322 (p90) REVERT: C 850 GLN cc_start: 0.9463 (OUTLIER) cc_final: 0.9095 (mm-40) REVERT: D 46 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8787 (tmm-80) REVERT: H 105 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7519 (p90) REVERT: L 6 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7164 (mt0) REVERT: L 47 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.7846 (mt) outliers start: 184 outliers final: 144 residues processed: 223 average time/residue: 0.3889 time to fit residues: 147.9856 Evaluate side-chains 206 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 45 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 613 ASN Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 910 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 348 TYR Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 834 TYR Chi-restraints excluded: chain C residue 837 CYS Chi-restraints excluded: chain C residue 850 GLN Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 105 PHE Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 118 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 273 optimal weight: 6.9990 chunk 242 optimal weight: 20.0000 chunk 388 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 232 optimal weight: 0.6980 chunk 361 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 267 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 GLN B 952 ASN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C 989 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.026523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.019606 restraints weight = 474728.960| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 4.98 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.724 32818 Z= 0.345 Angle : 0.894 74.150 44766 Z= 0.454 Chirality : 0.048 0.580 5167 Planarity : 0.005 0.132 5649 Dihedral : 11.176 110.621 5811 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.37 % Favored : 94.45 % Rotamer: Outliers : 4.55 % Allowed : 27.38 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3913 helix: 2.40 (0.19), residues: 705 sheet: -0.36 (0.17), residues: 935 loop : -0.83 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 433 HIS 0.014 0.001 HIS C 202 PHE 0.012 0.001 PHE C 65 TYR 0.030 0.001 TYR C 492 ARG 0.009 0.000 ARG J 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 45) link_NAG-ASN : angle 4.10375 ( 135) link_BETA1-4 : bond 0.00649 ( 27) link_BETA1-4 : angle 2.89970 ( 81) hydrogen bonds : bond 0.03916 ( 1151) hydrogen bonds : angle 5.84590 ( 3246) SS BOND : bond 0.00243 ( 48) SS BOND : angle 1.04009 ( 96) covalent geometry : bond 0.00951 (32698) covalent geometry : angle 0.85809 (44454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 45 time to evaluate : 3.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: 0.9153 (tpt) cc_final: 0.8419 (tmm) REVERT: B 255 TRP cc_start: 0.8336 (OUTLIER) cc_final: 0.7900 (m-90) REVERT: B 398 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8058 (m) REVERT: B 613 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8142 (m-40) REVERT: A 897 MET cc_start: 0.8731 (mtp) cc_final: 0.8390 (mtt) REVERT: A 910 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: C 350 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.8066 (p-90) REVERT: C 436 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7877 (m-40) REVERT: C 469 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8308 (pt) REVERT: C 730 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8629 (mtmm) REVERT: C 834 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8214 (p90) REVERT: E 40 MET cc_start: 0.9371 (mmm) cc_final: 0.9159 (mmm) REVERT: D 46 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8792 (tmm-80) REVERT: L 47 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8405 (tt) REVERT: L 61 ASP cc_start: 0.9317 (m-30) cc_final: 0.9116 (p0) outliers start: 156 outliers final: 124 residues processed: 195 average time/residue: 0.3942 time to fit residues: 132.7577 Evaluate side-chains 179 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 44 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 613 ASN Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 910 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 348 TYR Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 834 TYR Chi-restraints excluded: chain C residue 837 CYS Chi-restraints excluded: chain C residue 850 GLN Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 226 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 269 optimal weight: 8.9990 chunk 230 optimal weight: 20.0000 chunk 137 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 257 optimal weight: 40.0000 chunk 26 optimal weight: 7.9990 chunk 363 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1033 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.026398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.019457 restraints weight = 478073.934| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 4.99 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.723 32818 Z= 0.382 Angle : 0.914 74.119 44766 Z= 0.464 Chirality : 0.048 0.559 5167 Planarity : 0.005 0.132 5649 Dihedral : 10.979 110.149 5811 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.65 % Favored : 94.17 % Rotamer: Outliers : 4.49 % Allowed : 27.50 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3913 helix: 2.45 (0.20), residues: 692 sheet: -0.39 (0.17), residues: 976 loop : -0.84 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 433 HIS 0.013 0.001 HIS C 202 PHE 0.045 0.001 PHE H 105 TYR 0.028 0.002 TYR B 450 ARG 0.011 0.001 ARG J 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 45) link_NAG-ASN : angle 4.09794 ( 135) link_BETA1-4 : bond 0.00578 ( 27) link_BETA1-4 : angle 2.85937 ( 81) hydrogen bonds : bond 0.04072 ( 1151) hydrogen bonds : angle 5.91225 ( 3246) SS BOND : bond 0.00293 ( 48) SS BOND : angle 1.55687 ( 96) covalent geometry : bond 0.01012 (32698) covalent geometry : angle 0.87807 (44454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 44 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: 0.9322 (tpt) cc_final: 0.8587 (ppp) REVERT: B 255 TRP cc_start: 0.8372 (OUTLIER) cc_final: 0.7949 (m-90) REVERT: B 398 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8114 (m) REVERT: B 613 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8118 (m-40) REVERT: A 831 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7327 (mp) REVERT: A 897 MET cc_start: 0.9060 (mtp) cc_final: 0.8728 (mtt) REVERT: A 910 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8522 (pm20) REVERT: C 159 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8783 (p0) REVERT: C 350 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.7990 (p-90) REVERT: C 436 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7741 (m-40) REVERT: C 469 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8300 (pt) REVERT: C 730 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8626 (mtmm) REVERT: C 834 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8348 (p90) REVERT: C 850 GLN cc_start: 0.9460 (OUTLIER) cc_final: 0.9091 (mm-40) REVERT: E 40 MET cc_start: 0.9425 (mmm) cc_final: 0.9197 (mmm) REVERT: D 46 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8872 (tmm-80) REVERT: L 6 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.6920 (mt0) REVERT: L 61 ASP cc_start: 0.9431 (m-30) cc_final: 0.9180 (p0) outliers start: 154 outliers final: 134 residues processed: 193 average time/residue: 0.3812 time to fit residues: 130.8989 Evaluate side-chains 192 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 44 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 613 ASN Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 910 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 348 TYR Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 834 TYR Chi-restraints excluded: chain C residue 837 CYS Chi-restraints excluded: chain C residue 850 GLN Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 994 ILE Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 267 optimal weight: 0.0370 chunk 257 optimal weight: 40.0000 chunk 362 optimal weight: 8.9990 chunk 342 optimal weight: 8.9990 chunk 236 optimal weight: 0.0670 chunk 189 optimal weight: 6.9990 chunk 328 optimal weight: 30.0000 chunk 323 optimal weight: 9.9990 chunk 371 optimal weight: 30.0000 chunk 240 optimal weight: 7.9990 chunk 350 optimal weight: 0.7980 overall best weight: 3.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.026538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.019593 restraints weight = 475424.084| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 5.03 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.724 32818 Z= 0.340 Angle : 0.888 74.155 44766 Z= 0.452 Chirality : 0.047 0.547 5167 Planarity : 0.005 0.130 5649 Dihedral : 10.690 110.148 5811 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.34 % Favored : 94.45 % Rotamer: Outliers : 4.20 % Allowed : 27.79 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3913 helix: 2.46 (0.20), residues: 694 sheet: -0.35 (0.17), residues: 970 loop : -0.85 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 433 HIS 0.012 0.001 HIS C 202 PHE 0.041 0.001 PHE H 105 TYR 0.029 0.001 TYR C 492 ARG 0.010 0.000 ARG J 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 45) link_NAG-ASN : angle 4.02972 ( 135) link_BETA1-4 : bond 0.00660 ( 27) link_BETA1-4 : angle 2.88443 ( 81) hydrogen bonds : bond 0.03841 ( 1151) hydrogen bonds : angle 5.75412 ( 3246) SS BOND : bond 0.00225 ( 48) SS BOND : angle 1.36358 ( 96) covalent geometry : bond 0.00944 (32698) covalent geometry : angle 0.85145 (44454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7826 Ramachandran restraints generated. 3913 Oldfield, 0 Emsley, 3913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 44 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: 0.9199 (tpt) cc_final: 0.8454 (ppp) REVERT: B 255 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7911 (m-90) REVERT: B 398 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.7981 (m) REVERT: B 613 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8158 (m-40) REVERT: A 897 MET cc_start: 0.8601 (mtp) cc_final: 0.8400 (mtt) REVERT: A 910 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: C 159 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8786 (p0) REVERT: C 350 TRP cc_start: 0.8670 (OUTLIER) cc_final: 0.8055 (p-90) REVERT: C 436 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7795 (m-40) REVERT: C 469 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8361 (pt) REVERT: C 730 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8626 (mtmm) REVERT: C 834 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8204 (p90) REVERT: E 40 MET cc_start: 0.9399 (mmm) cc_final: 0.9172 (mmm) REVERT: D 46 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8777 (tmm-80) REVERT: L 6 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: L 61 ASP cc_start: 0.9313 (m-30) cc_final: 0.9033 (p0) outliers start: 144 outliers final: 125 residues processed: 181 average time/residue: 0.3779 time to fit residues: 121.8654 Evaluate side-chains 181 residues out of total 3438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 44 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 613 ASN Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 848 CYS Chi-restraints excluded: chain A residue 910 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 348 TYR Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 730 LYS Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 834 TYR Chi-restraints excluded: chain C residue 837 CYS Chi-restraints excluded: chain C residue 850 GLN Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 159 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 342 optimal weight: 8.9990 chunk 257 optimal weight: 40.0000 chunk 355 optimal weight: 10.0000 chunk 368 optimal weight: 4.9990 chunk 144 optimal weight: 0.0980 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.026375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.019545 restraints weight = 475124.175| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.83 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.724 32818 Z= 0.366 Angle : 0.897 74.131 44766 Z= 0.457 Chirality : 0.047 0.527 5167 Planarity : 0.005 0.130 5649 Dihedral : 10.537 109.670 5811 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.22 % Rotamer: Outliers : 4.20 % Allowed : 27.82 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3913 helix: 2.45 (0.20), residues: 693 sheet: -0.38 (0.16), residues: 990 loop : -0.82 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 433 HIS 0.011 0.001 HIS C 202 PHE 0.037 0.001 PHE H 105 TYR 0.028 0.001 TYR B 450 ARG 0.008 0.000 ARG J 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 45) link_NAG-ASN : angle 3.99349 ( 135) link_BETA1-4 : bond 0.00582 ( 27) link_BETA1-4 : angle 2.82239 ( 81) hydrogen bonds : bond 0.03956 ( 1151) hydrogen bonds : angle 5.79445 ( 3246) SS BOND : bond 0.00271 ( 48) SS BOND : angle 1.33287 ( 96) covalent geometry : bond 0.00986 (32698) covalent geometry : angle 0.86186 (44454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13050.26 seconds wall clock time: 227 minutes 27.69 seconds (13647.69 seconds total)