Starting phenix.real_space_refine on Mon Jun 23 06:39:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybi_33722/06_2025/7ybi_33722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybi_33722/06_2025/7ybi_33722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ybi_33722/06_2025/7ybi_33722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybi_33722/06_2025/7ybi_33722.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybi_33722/06_2025/7ybi_33722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybi_33722/06_2025/7ybi_33722.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 114 5.16 5 C 16930 2.51 5 N 4312 2.21 5 O 5293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.84s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26649 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8430 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8450 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1028} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8469 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 52, 'TRANS': 1029} Chain breaks: 5 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.05, per 1000 atoms: 0.64 Number of scatterers: 26649 At special positions: 0 Unit cell: (152.88, 148.72, 215.28, 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 114 16.00 O 5293 8.00 N 4312 7.00 C 16930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1406 " - " ASN A 282 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 657 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 7.82 Conformation dependent library (CDL) restraints added in 3.4 seconds 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 26.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.906A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.160A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.715A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.054A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.741A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.633A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.547A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.605A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.620A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.509A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.779A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.550A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 987 through 1032 removed outlier: 3.718A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1159 removed outlier: 4.357A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A1154 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.562A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.579A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.571A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.657A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.560A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.895A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.711A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.363A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1161 removed outlier: 4.176A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.199A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.820A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.422A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.856A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.552A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.030A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.787A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.621A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.590A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.642A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 3.898A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.799A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.721A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.690A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.416A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.564A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.869A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 642 through 645 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.620A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.070A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.859A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.859A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.085A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.811A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.873A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.594A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 133 through 143 removed outlier: 8.661A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.676A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.549A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.524A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.693A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AD1, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.397A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 703 through 704 removed outlier: 6.780A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.536A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 3.930A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.807A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.061A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.292A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 141 through 143 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.109A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.649A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.531A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.053A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.523A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.714A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.318A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.318A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.935A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 982 hydrogen bonds defined for protein. 2697 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: 12.83 Time building geometry restraints manager: 9.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4479 1.32 - 1.45: 7647 1.45 - 1.57: 14961 1.57 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 27231 Sorted by residual: bond pdb=" C PRO B 621 " pdb=" O PRO B 621 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.30e-02 5.92e+03 7.51e+00 bond pdb=" N VAL B 622 " pdb=" CA VAL B 622 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.02e+00 bond pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.35e-02 5.49e+03 6.31e+00 bond pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 1.461 1.491 -0.029 1.23e-02 6.61e+03 5.75e+00 bond pdb=" C5 MAN e 3 " pdb=" O5 MAN e 3 " ideal model delta sigma weight residual 1.418 1.464 -0.046 2.00e-02 2.50e+03 5.26e+00 ... (remaining 27226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 36425 2.30 - 4.61: 549 4.61 - 6.91: 49 6.91 - 9.21: 7 9.21 - 11.52: 1 Bond angle restraints: 37031 Sorted by residual: angle pdb=" C ASN A 148 " pdb=" N ASN A 149 " pdb=" CA ASN A 149 " ideal model delta sigma weight residual 122.65 111.13 11.52 1.66e+00 3.63e-01 4.81e+01 angle pdb=" C HIS A 146 " pdb=" N LYS A 147 " pdb=" CA LYS A 147 " ideal model delta sigma weight residual 121.90 115.59 6.31 1.26e+00 6.30e-01 2.51e+01 angle pdb=" C VAL A 860 " pdb=" N LEU A 861 " pdb=" CA LEU A 861 " ideal model delta sigma weight residual 121.61 114.94 6.67 1.39e+00 5.18e-01 2.30e+01 angle pdb=" N ILE B 909 " pdb=" CA ILE B 909 " pdb=" C ILE B 909 " ideal model delta sigma weight residual 112.29 107.88 4.41 9.40e-01 1.13e+00 2.20e+01 angle pdb=" C PRO B 621 " pdb=" CA PRO B 621 " pdb=" CB PRO B 621 " ideal model delta sigma weight residual 111.56 105.39 6.17 1.65e+00 3.67e-01 1.40e+01 ... (remaining 37026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 16453 24.59 - 49.18: 799 49.18 - 73.76: 136 73.76 - 98.35: 47 98.35 - 122.94: 21 Dihedral angle restraints: 17456 sinusoidal: 8022 harmonic: 9434 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 0.46 -86.46 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -162.36 76.36 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -156.50 70.50 1 1.00e+01 1.00e-02 6.40e+01 ... (remaining 17453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 4322 0.108 - 0.217: 130 0.217 - 0.325: 8 0.325 - 0.434: 0 0.434 - 0.542: 3 Chirality restraints: 4463 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C1 NAG A1401 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1401 " pdb=" O5 NAG A1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 4460 not shown) Planarity restraints: 4710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1078 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO C1079 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO C1079 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C1079 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 855 " -0.012 2.00e-02 2.50e+03 1.44e-02 3.64e+00 pdb=" CG PHE A 855 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 855 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 855 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 855 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 855 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 855 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 229 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.23e+00 pdb=" N PRO C 230 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " 0.025 5.00e-02 4.00e+02 ... (remaining 4707 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 396 2.61 - 3.18: 24094 3.18 - 3.76: 41351 3.76 - 4.33: 56446 4.33 - 4.90: 90562 Nonbonded interactions: 212849 Sorted by model distance: nonbonded pdb=" O ASP C 290 " pdb=" OG SER C 297 " model vdw 2.038 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.104 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.136 3.040 nonbonded pdb=" OD1 ASN B 125 " pdb=" OG SER B 172 " model vdw 2.153 3.040 nonbonded pdb=" O ARG B 214 " pdb=" OH TYR B 266 " model vdw 2.166 3.040 ... (remaining 212844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 622 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1408)) selection = (chain 'B' and (resid 14 through 622 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1408)) selection = (chain 'C' and (resid 14 through 621 or resid 635 or resid 641 through 826 or re \ sid 855 through 1162 or resid 1401 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 66.360 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.004 0.071 27364 Z= 0.197 Angle : 0.693 17.638 37388 Z= 0.337 Chirality : 0.048 0.542 4463 Planarity : 0.004 0.100 4657 Dihedral : 15.194 122.938 11258 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.84 % Favored : 96.07 % Rotamer: Outliers : 0.21 % Allowed : 0.18 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.14), residues: 3205 helix: 0.62 (0.20), residues: 699 sheet: -0.10 (0.22), residues: 587 loop : -1.25 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 633 HIS 0.011 0.001 HIS B1048 PHE 0.033 0.001 PHE A 855 TYR 0.016 0.001 TYR C 495 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 53) link_NAG-ASN : angle 3.25092 ( 159) link_ALPHA1-4 : bond 0.00654 ( 6) link_ALPHA1-4 : angle 1.80399 ( 18) link_BETA1-4 : bond 0.00484 ( 29) link_BETA1-4 : angle 1.16615 ( 87) hydrogen bonds : bond 0.26928 ( 969) hydrogen bonds : angle 9.71402 ( 2697) link_BETA1-6 : bond 0.00448 ( 3) link_BETA1-6 : angle 1.50740 ( 9) SS BOND : bond 0.00262 ( 42) SS BOND : angle 1.01541 ( 84) covalent geometry : bond 0.00396 (27231) covalent geometry : angle 0.65763 (37031) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8388 (m-90) cc_final: 0.8172 (m-90) REVERT: A 732 THR cc_start: 0.9002 (m) cc_final: 0.8715 (p) REVERT: C 87 ASN cc_start: 0.6047 (p0) cc_final: 0.5835 (m-40) REVERT: C 360 ASN cc_start: 0.8541 (t0) cc_final: 0.8174 (t0) REVERT: C 731 MET cc_start: 0.8412 (ptp) cc_final: 0.8047 (ptp) REVERT: C 922 LEU cc_start: 0.8327 (mt) cc_final: 0.8095 (mt) outliers start: 6 outliers final: 1 residues processed: 258 average time/residue: 0.3405 time to fit residues: 149.4034 Evaluate side-chains 178 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 0.0980 chunk 244 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 293 optimal weight: 0.6980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1119 ASN B 901 GLN B 913 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.117113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.090812 restraints weight = 101098.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090035 restraints weight = 97605.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090502 restraints weight = 79114.969| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27364 Z= 0.158 Angle : 0.661 16.100 37388 Z= 0.327 Chirality : 0.047 0.503 4463 Planarity : 0.004 0.072 4657 Dihedral : 11.452 111.108 5436 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 0.07 % Allowed : 4.76 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.14), residues: 3205 helix: 0.94 (0.19), residues: 720 sheet: -0.13 (0.21), residues: 632 loop : -1.29 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.007 0.001 HIS A1159 PHE 0.020 0.001 PHE A 565 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.001 ARG C 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 53) link_NAG-ASN : angle 3.14478 ( 159) link_ALPHA1-4 : bond 0.01404 ( 6) link_ALPHA1-4 : angle 2.50550 ( 18) link_BETA1-4 : bond 0.00533 ( 29) link_BETA1-4 : angle 1.15578 ( 87) hydrogen bonds : bond 0.05464 ( 969) hydrogen bonds : angle 6.98043 ( 2697) link_BETA1-6 : bond 0.01246 ( 3) link_BETA1-6 : angle 1.89389 ( 9) SS BOND : bond 0.00325 ( 42) SS BOND : angle 1.09773 ( 84) covalent geometry : bond 0.00339 (27231) covalent geometry : angle 0.62336 (37031) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 255 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7796 (p90) cc_final: 0.7520 (p90) REVERT: A 872 GLN cc_start: 0.8224 (tt0) cc_final: 0.8020 (tt0) REVERT: B 513 LEU cc_start: 0.9194 (tp) cc_final: 0.8945 (tp) REVERT: B 619 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7538 (mm-30) REVERT: C 360 ASN cc_start: 0.8665 (t0) cc_final: 0.8300 (t0) REVERT: C 731 MET cc_start: 0.8857 (ptp) cc_final: 0.8420 (ptp) outliers start: 2 outliers final: 0 residues processed: 257 average time/residue: 0.3477 time to fit residues: 151.1701 Evaluate side-chains 177 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 chunk 231 optimal weight: 30.0000 chunk 102 optimal weight: 4.9990 chunk 275 optimal weight: 8.9990 chunk 149 optimal weight: 0.4980 chunk 300 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 777 ASN B 913 GLN C 185 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 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 = 0.4062 r_free = 0.4062 target = 0.116323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.089605 restraints weight = 101009.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.088821 restraints weight = 95870.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089277 restraints weight = 77089.462| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27364 Z= 0.184 Angle : 0.675 19.367 37388 Z= 0.326 Chirality : 0.047 0.507 4463 Planarity : 0.004 0.075 4657 Dihedral : 10.594 108.349 5436 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.87 (0.14), residues: 3205 helix: 1.03 (0.19), residues: 715 sheet: -0.37 (0.21), residues: 631 loop : -1.34 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 64 HIS 0.008 0.001 HIS B 66 PHE 0.019 0.002 PHE C 275 TYR 0.018 0.002 TYR A 756 ARG 0.005 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 53) link_NAG-ASN : angle 3.23582 ( 159) link_ALPHA1-4 : bond 0.01572 ( 6) link_ALPHA1-4 : angle 2.77415 ( 18) link_BETA1-4 : bond 0.00457 ( 29) link_BETA1-4 : angle 1.21939 ( 87) hydrogen bonds : bond 0.04958 ( 969) hydrogen bonds : angle 6.54482 ( 2697) link_BETA1-6 : bond 0.01343 ( 3) link_BETA1-6 : angle 2.17674 ( 9) SS BOND : bond 0.00520 ( 42) SS BOND : angle 1.19629 ( 84) covalent geometry : bond 0.00400 (27231) covalent geometry : angle 0.63490 (37031) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 3.021 Fit side-chains revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8043 (mpp-170) cc_final: 0.7754 (mpp-170) REVERT: A 780 GLU cc_start: 0.8312 (tp30) cc_final: 0.7849 (tp30) REVERT: A 1029 MET cc_start: 0.9291 (tpp) cc_final: 0.9032 (mmm) REVERT: B 619 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 1019 ARG cc_start: 0.8664 (tpp-160) cc_final: 0.8381 (tpt170) REVERT: B 1050 MET cc_start: 0.7703 (ptp) cc_final: 0.7491 (ptp) REVERT: C 360 ASN cc_start: 0.8692 (t0) cc_final: 0.8345 (t0) REVERT: C 731 MET cc_start: 0.8826 (ptp) cc_final: 0.8412 (ptp) REVERT: C 740 MET cc_start: 0.7765 (tpt) cc_final: 0.7539 (tpp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3353 time to fit residues: 134.4538 Evaluate side-chains 170 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 60 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 257 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 935 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 = 0.4067 r_free = 0.4067 target = 0.116588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.090096 restraints weight = 102067.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.089240 restraints weight = 95563.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.089514 restraints weight = 79580.405| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27364 Z= 0.157 Angle : 0.656 17.743 37388 Z= 0.315 Chirality : 0.047 0.497 4463 Planarity : 0.004 0.072 4657 Dihedral : 9.716 106.752 5436 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.14), residues: 3205 helix: 1.08 (0.19), residues: 719 sheet: -0.49 (0.20), residues: 655 loop : -1.33 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.006 0.001 HIS C 519 PHE 0.021 0.002 PHE C 592 TYR 0.015 0.001 TYR B1067 ARG 0.004 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 53) link_NAG-ASN : angle 3.23543 ( 159) link_ALPHA1-4 : bond 0.01724 ( 6) link_ALPHA1-4 : angle 2.94956 ( 18) link_BETA1-4 : bond 0.00433 ( 29) link_BETA1-4 : angle 1.16068 ( 87) hydrogen bonds : bond 0.04388 ( 969) hydrogen bonds : angle 6.32759 ( 2697) link_BETA1-6 : bond 0.01395 ( 3) link_BETA1-6 : angle 2.11416 ( 9) SS BOND : bond 0.00314 ( 42) SS BOND : angle 1.14460 ( 84) covalent geometry : bond 0.00343 (27231) covalent geometry : angle 0.61484 (37031) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8250 (tp30) cc_final: 0.7778 (tp30) REVERT: A 1029 MET cc_start: 0.9243 (tpp) cc_final: 0.9017 (mmm) REVERT: B 177 MET cc_start: -0.0648 (mtm) cc_final: -0.2176 (ttp) REVERT: C 360 ASN cc_start: 0.8710 (t0) cc_final: 0.8336 (t0) REVERT: C 731 MET cc_start: 0.8855 (ptp) cc_final: 0.8435 (ptp) REVERT: C 740 MET cc_start: 0.7815 (tpt) cc_final: 0.7547 (tpp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.3494 time to fit residues: 150.5861 Evaluate side-chains 172 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 255 optimal weight: 20.0000 chunk 277 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 100 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 15 optimal weight: 0.0040 chunk 109 optimal weight: 8.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 913 GLN C 913 GLN C 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.117763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.091974 restraints weight = 101534.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.091927 restraints weight = 85322.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092103 restraints weight = 72621.166| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27364 Z= 0.124 Angle : 0.633 17.611 37388 Z= 0.301 Chirality : 0.047 0.502 4463 Planarity : 0.004 0.067 4657 Dihedral : 8.885 103.781 5436 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.15), residues: 3205 helix: 1.20 (0.19), residues: 714 sheet: -0.46 (0.20), residues: 665 loop : -1.22 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.007 0.001 HIS C 519 PHE 0.025 0.001 PHE C 392 TYR 0.013 0.001 TYR C 495 ARG 0.004 0.000 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 53) link_NAG-ASN : angle 3.12687 ( 159) link_ALPHA1-4 : bond 0.01748 ( 6) link_ALPHA1-4 : angle 3.10577 ( 18) link_BETA1-4 : bond 0.00435 ( 29) link_BETA1-4 : angle 1.16233 ( 87) hydrogen bonds : bond 0.04065 ( 969) hydrogen bonds : angle 6.07094 ( 2697) link_BETA1-6 : bond 0.01567 ( 3) link_BETA1-6 : angle 2.07390 ( 9) SS BOND : bond 0.00269 ( 42) SS BOND : angle 1.14026 ( 84) covalent geometry : bond 0.00266 (27231) covalent geometry : angle 0.59262 (37031) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3748 (tmm) cc_final: 0.3486 (tmm) REVERT: A 238 PHE cc_start: 0.7812 (p90) cc_final: 0.7460 (p90) REVERT: A 663 ASP cc_start: 0.7192 (t70) cc_final: 0.6968 (t0) REVERT: A 902 MET cc_start: 0.9075 (mmp) cc_final: 0.8874 (mmp) REVERT: B 177 MET cc_start: -0.0846 (mtm) cc_final: -0.1615 (mtm) REVERT: B 774 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8665 (mm-40) REVERT: C 360 ASN cc_start: 0.8658 (t0) cc_final: 0.8276 (t0) REVERT: C 731 MET cc_start: 0.8873 (ptp) cc_final: 0.8462 (ptp) REVERT: C 740 MET cc_start: 0.7825 (tpt) cc_final: 0.7569 (tpp) REVERT: C 864 LEU cc_start: 0.8729 (tp) cc_final: 0.8432 (tt) REVERT: C 1002 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7679 (tm-30) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3365 time to fit residues: 146.6541 Evaluate side-chains 177 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 229 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 268 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 145 ASN B 913 GLN B 955 ASN C 343 ASN C 913 GLN C 955 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.115779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089408 restraints weight = 101422.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088511 restraints weight = 96460.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.088925 restraints weight = 80422.674| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27364 Z= 0.185 Angle : 0.671 17.225 37388 Z= 0.321 Chirality : 0.048 0.519 4463 Planarity : 0.004 0.067 4657 Dihedral : 8.376 104.735 5436 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.15), residues: 3205 helix: 1.15 (0.19), residues: 716 sheet: -0.54 (0.20), residues: 649 loop : -1.32 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.006 0.001 HIS C 519 PHE 0.022 0.002 PHE C 275 TYR 0.016 0.001 TYR B1067 ARG 0.005 0.001 ARG A 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00682 ( 53) link_NAG-ASN : angle 3.25448 ( 159) link_ALPHA1-4 : bond 0.01854 ( 6) link_ALPHA1-4 : angle 3.33854 ( 18) link_BETA1-4 : bond 0.00423 ( 29) link_BETA1-4 : angle 1.21200 ( 87) hydrogen bonds : bond 0.04169 ( 969) hydrogen bonds : angle 6.10805 ( 2697) link_BETA1-6 : bond 0.01574 ( 3) link_BETA1-6 : angle 1.76961 ( 9) SS BOND : bond 0.00333 ( 42) SS BOND : angle 1.21325 ( 84) covalent geometry : bond 0.00405 (27231) covalent geometry : angle 0.62915 (37031) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.7091 (t70) cc_final: 0.6765 (t0) REVERT: A 902 MET cc_start: 0.9250 (mmp) cc_final: 0.8967 (mmp) REVERT: B 153 MET cc_start: 0.2993 (ppp) cc_final: 0.1774 (tpt) REVERT: B 177 MET cc_start: -0.0656 (mtm) cc_final: -0.1342 (mtm) REVERT: B 374 PHE cc_start: 0.7423 (m-80) cc_final: 0.7210 (m-10) REVERT: C 129 LYS cc_start: 0.7720 (tptt) cc_final: 0.7100 (tttm) REVERT: C 360 ASN cc_start: 0.8732 (t0) cc_final: 0.8331 (t0) REVERT: C 731 MET cc_start: 0.8928 (ptp) cc_final: 0.8555 (ptp) REVERT: C 864 LEU cc_start: 0.8786 (tp) cc_final: 0.8442 (tt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3193 time to fit residues: 128.5833 Evaluate side-chains 171 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 299 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 228 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 293 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.115257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.089306 restraints weight = 101704.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.088413 restraints weight = 98703.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.088875 restraints weight = 81079.818| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27364 Z= 0.194 Angle : 0.685 17.003 37388 Z= 0.328 Chirality : 0.048 0.504 4463 Planarity : 0.004 0.065 4657 Dihedral : 8.108 104.828 5436 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.14), residues: 3205 helix: 1.12 (0.19), residues: 720 sheet: -0.64 (0.20), residues: 645 loop : -1.40 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 633 HIS 0.006 0.001 HIS C 519 PHE 0.025 0.002 PHE C 275 TYR 0.016 0.002 TYR B1067 ARG 0.013 0.001 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 53) link_NAG-ASN : angle 3.24695 ( 159) link_ALPHA1-4 : bond 0.01762 ( 6) link_ALPHA1-4 : angle 3.42029 ( 18) link_BETA1-4 : bond 0.00425 ( 29) link_BETA1-4 : angle 1.24336 ( 87) hydrogen bonds : bond 0.04163 ( 969) hydrogen bonds : angle 6.13812 ( 2697) link_BETA1-6 : bond 0.01526 ( 3) link_BETA1-6 : angle 1.40789 ( 9) SS BOND : bond 0.00321 ( 42) SS BOND : angle 1.55142 ( 84) covalent geometry : bond 0.00423 (27231) covalent geometry : angle 0.64236 (37031) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.7137 (t70) cc_final: 0.6744 (t0) REVERT: A 902 MET cc_start: 0.9288 (mmp) cc_final: 0.9009 (mmp) REVERT: A 1050 MET cc_start: 0.7588 (ptt) cc_final: 0.7213 (ptt) REVERT: B 153 MET cc_start: 0.3060 (ppp) cc_final: 0.1799 (tpt) REVERT: B 177 MET cc_start: -0.0345 (mtm) cc_final: -0.1011 (mtm) REVERT: C 129 LYS cc_start: 0.7714 (tptt) cc_final: 0.7116 (tttm) REVERT: C 360 ASN cc_start: 0.8759 (t0) cc_final: 0.8349 (t0) REVERT: C 731 MET cc_start: 0.8966 (ptp) cc_final: 0.8592 (ptp) REVERT: C 864 LEU cc_start: 0.8824 (tp) cc_final: 0.8397 (tt) REVERT: C 878 LEU cc_start: 0.9218 (tp) cc_final: 0.9010 (tt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.3329 time to fit residues: 134.4929 Evaluate side-chains 169 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 65 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 300 optimal weight: 0.7980 chunk 236 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 913 GLN B 955 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.114119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.088741 restraints weight = 101788.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.088456 restraints weight = 97067.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089114 restraints weight = 76620.944| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27364 Z= 0.225 Angle : 0.719 16.949 37388 Z= 0.348 Chirality : 0.049 0.502 4463 Planarity : 0.004 0.067 4657 Dihedral : 8.104 106.182 5436 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.14), residues: 3205 helix: 0.93 (0.19), residues: 719 sheet: -0.72 (0.20), residues: 660 loop : -1.51 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 633 HIS 0.010 0.001 HIS C 519 PHE 0.039 0.002 PHE B 559 TYR 0.026 0.002 TYR C 91 ARG 0.009 0.001 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00682 ( 53) link_NAG-ASN : angle 3.26755 ( 159) link_ALPHA1-4 : bond 0.01766 ( 6) link_ALPHA1-4 : angle 3.41803 ( 18) link_BETA1-4 : bond 0.00423 ( 29) link_BETA1-4 : angle 1.32582 ( 87) hydrogen bonds : bond 0.04281 ( 969) hydrogen bonds : angle 6.27671 ( 2697) link_BETA1-6 : bond 0.01202 ( 3) link_BETA1-6 : angle 1.26806 ( 9) SS BOND : bond 0.00357 ( 42) SS BOND : angle 1.41304 ( 84) covalent geometry : bond 0.00494 (27231) covalent geometry : angle 0.67964 (37031) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.7159 (t70) cc_final: 0.6687 (t0) REVERT: B 177 MET cc_start: -0.0287 (mtm) cc_final: -0.0716 (mtm) REVERT: C 129 LYS cc_start: 0.7711 (tptt) cc_final: 0.7092 (tttm) REVERT: C 360 ASN cc_start: 0.8714 (t0) cc_final: 0.8293 (t0) REVERT: C 731 MET cc_start: 0.9009 (ptp) cc_final: 0.8646 (ptp) REVERT: C 864 LEU cc_start: 0.8824 (tp) cc_final: 0.8439 (tp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3450 time to fit residues: 132.2982 Evaluate side-chains 156 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 148 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 314 optimal weight: 0.9990 chunk 253 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 258 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN A 474 GLN A 935 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1054 GLN B1125 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.117194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.090549 restraints weight = 101286.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.090062 restraints weight = 92683.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.090411 restraints weight = 77871.799| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27364 Z= 0.121 Angle : 0.653 16.664 37388 Z= 0.312 Chirality : 0.047 0.487 4463 Planarity : 0.004 0.065 4657 Dihedral : 7.486 101.522 5436 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 0.04 % Allowed : 0.60 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.14), residues: 3205 helix: 1.21 (0.20), residues: 709 sheet: -0.62 (0.20), residues: 657 loop : -1.36 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.001 PHE C 275 TYR 0.018 0.001 TYR C 380 ARG 0.010 0.000 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 53) link_NAG-ASN : angle 3.06525 ( 159) link_ALPHA1-4 : bond 0.01721 ( 6) link_ALPHA1-4 : angle 3.32793 ( 18) link_BETA1-4 : bond 0.00431 ( 29) link_BETA1-4 : angle 1.22092 ( 87) hydrogen bonds : bond 0.03897 ( 969) hydrogen bonds : angle 5.97614 ( 2697) link_BETA1-6 : bond 0.01174 ( 3) link_BETA1-6 : angle 1.28109 ( 9) SS BOND : bond 0.00253 ( 42) SS BOND : angle 1.25563 ( 84) covalent geometry : bond 0.00261 (27231) covalent geometry : angle 0.61472 (37031) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.7040 (t70) cc_final: 0.6590 (t0) REVERT: A 902 MET cc_start: 0.9262 (mmp) cc_final: 0.9023 (mmt) REVERT: B 153 MET cc_start: 0.3185 (ppp) cc_final: 0.2191 (tpt) REVERT: B 177 MET cc_start: -0.0375 (mtm) cc_final: -0.0797 (mtm) REVERT: B 586 ASP cc_start: 0.7322 (t0) cc_final: 0.7113 (t0) REVERT: B 774 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8679 (mm-40) REVERT: B 777 ASN cc_start: 0.9173 (m110) cc_final: 0.8870 (m110) REVERT: C 360 ASN cc_start: 0.8777 (t0) cc_final: 0.8378 (t0) REVERT: C 731 MET cc_start: 0.8891 (ptp) cc_final: 0.8596 (ptp) REVERT: C 864 LEU cc_start: 0.8720 (tp) cc_final: 0.8274 (tt) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.3333 time to fit residues: 136.2398 Evaluate side-chains 175 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 248 optimal weight: 10.0000 chunk 290 optimal weight: 3.9990 chunk 293 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 913 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.113158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.087036 restraints weight = 101607.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086065 restraints weight = 101678.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086453 restraints weight = 90980.803| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 27364 Z= 0.274 Angle : 0.768 16.770 37388 Z= 0.373 Chirality : 0.050 0.500 4463 Planarity : 0.004 0.064 4657 Dihedral : 8.008 106.605 5436 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.61 % Favored : 93.35 % Rotamer: Outliers : 0.07 % Allowed : 0.64 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.27 (0.14), residues: 3205 helix: 0.80 (0.19), residues: 719 sheet: -0.80 (0.20), residues: 644 loop : -1.58 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 633 HIS 0.008 0.001 HIS A1064 PHE 0.025 0.002 PHE C1042 TYR 0.021 0.002 TYR C 421 ARG 0.009 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 53) link_NAG-ASN : angle 3.26698 ( 159) link_ALPHA1-4 : bond 0.01730 ( 6) link_ALPHA1-4 : angle 3.32477 ( 18) link_BETA1-4 : bond 0.00430 ( 29) link_BETA1-4 : angle 1.39518 ( 87) hydrogen bonds : bond 0.04446 ( 969) hydrogen bonds : angle 6.33580 ( 2697) link_BETA1-6 : bond 0.00948 ( 3) link_BETA1-6 : angle 1.20977 ( 9) SS BOND : bond 0.00415 ( 42) SS BOND : angle 1.47192 ( 84) covalent geometry : bond 0.00604 (27231) covalent geometry : angle 0.73154 (37031) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6410 Ramachandran restraints generated. 3205 Oldfield, 0 Emsley, 3205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.7241 (t70) cc_final: 0.6723 (t0) REVERT: B 153 MET cc_start: 0.2917 (ppp) cc_final: 0.1815 (tpt) REVERT: B 177 MET cc_start: 0.0029 (mtm) cc_final: -0.1014 (ttp) REVERT: B 777 ASN cc_start: 0.9215 (m110) cc_final: 0.8950 (m110) REVERT: C 129 LYS cc_start: 0.7740 (tptt) cc_final: 0.7223 (ttmm) REVERT: C 360 ASN cc_start: 0.8726 (t0) cc_final: 0.8289 (t0) REVERT: C 731 MET cc_start: 0.8955 (ptp) cc_final: 0.8586 (ptp) REVERT: C 864 LEU cc_start: 0.8821 (tp) cc_final: 0.8441 (tp) outliers start: 2 outliers final: 0 residues processed: 220 average time/residue: 0.3501 time to fit residues: 129.3454 Evaluate side-chains 150 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 77 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 306 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 224 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 246 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN A 784 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.116868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.090952 restraints weight = 100884.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090338 restraints weight = 96461.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.090590 restraints weight = 79737.042| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27364 Z= 0.121 Angle : 0.652 16.546 37388 Z= 0.313 Chirality : 0.048 0.484 4463 Planarity : 0.004 0.062 4657 Dihedral : 7.343 101.108 5436 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.02 (0.14), residues: 3205 helix: 1.09 (0.19), residues: 719 sheet: -0.70 (0.20), residues: 653 loop : -1.44 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 64 HIS 0.005 0.001 HIS A1048 PHE 0.022 0.001 PHE C 275 TYR 0.022 0.001 TYR C 380 ARG 0.006 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 53) link_NAG-ASN : angle 3.03821 ( 159) link_ALPHA1-4 : bond 0.01646 ( 6) link_ALPHA1-4 : angle 3.20540 ( 18) link_BETA1-4 : bond 0.00430 ( 29) link_BETA1-4 : angle 1.22412 ( 87) hydrogen bonds : bond 0.03872 ( 969) hydrogen bonds : angle 5.94811 ( 2697) link_BETA1-6 : bond 0.00972 ( 3) link_BETA1-6 : angle 1.22143 ( 9) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.17267 ( 84) covalent geometry : bond 0.00262 (27231) covalent geometry : angle 0.61437 (37031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7520.84 seconds wall clock time: 133 minutes 38.45 seconds (8018.45 seconds total)