Starting phenix.real_space_refine on Fri Mar 6 00:47:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e7d_30999/03_2026/7e7d_30999.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e7d_30999/03_2026/7e7d_30999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e7d_30999/03_2026/7e7d_30999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e7d_30999/03_2026/7e7d_30999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e7d_30999/03_2026/7e7d_30999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e7d_30999/03_2026/7e7d_30999.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16855 2.51 5 N 4301 2.21 5 O 5236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26509 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 8429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8429 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 51, 'TRANS': 1028} Chain breaks: 6 Chain: "B" Number of atoms: 8429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8429 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 51, 'TRANS': 1028} Chain breaks: 6 Chain: "C" Number of atoms: 8429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8429 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 51, 'TRANS': 1028} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 124 Unusual residues: {'ELA': 2, 'NAG': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {'ELA': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.15, per 1000 atoms: 0.19 Number of scatterers: 26509 At special positions: 0 Unit cell: (129.353, 141.31, 175.007, 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 117 16.00 O 5236 8.00 N 4301 7.00 C 16855 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=2.04 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 617 " - pdb=" SG CYS A 649 " distance=2.04 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 A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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 B 840 " - pdb=" SG CYS B 851 " 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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 C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG 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 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 c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A1601 " - " ASN A 343 " " NAG A1602 " - " ASN A 331 " " NAG A1603 " - " ASN A 603 " " NAG A1604 " - " ASN A 657 " " NAG A1605 " - " ASN A 17 " " NAG A1608 " - " ASN A 61 " " NAG B1602 " - " ASN B 343 " " NAG B1603 " - " ASN B 331 " " NAG B1604 " - " ASN B 603 " " NAG B1605 " - " ASN B 657 " " NAG B1606 " - " ASN B 17 " " NAG B1607 " - " ASN B 61 " " NAG C1601 " - " ASN C 343 " " NAG C1602 " - " ASN C 331 " " NAG C1603 " - " ASN C 603 " " NAG C1604 " - " ASN C 657 " " NAG C1605 " - " ASN C 17 " " NAG C1606 " - " ASN C 61 " " NAG C1607 " - " ASN C 616 " " NAG D 1 " - " ASN B 717 " " NAG E 1 " - " ASN A 616 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 122 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 709 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A1074 " " NAG P 1 " - " ASN B 616 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN B 122 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B 709 " " NAG Y 1 " - " ASN B 165 " " NAG Z 1 " - " ASN B1074 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " " NAG f 1 " - " ASN C 282 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 122 " " NAG i 1 " - " ASN C 801 " " NAG j 1 " - " ASN C 709 " " NAG k 1 " - " ASN C 165 " " NAG l 1 " - " ASN C1074 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.0 seconds 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 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: 82 helices and 51 sheets defined 28.2% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.652A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.627A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.749A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.547A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.659A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 843 through 848' Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.848A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.145A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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 985 through 1033 removed outlier: 4.278A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.045A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (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 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.652A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.627A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 639 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.749A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.547A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.848A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.145A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (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 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.278A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.044A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.652A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.626A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (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 502 through 505 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 639 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.749A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.547A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 843 through 848 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.849A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.145A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.278A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.044A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.962A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.962A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.596A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.548A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.527A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.712A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.116A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.492A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.455A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.969A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.613A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.968A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.968A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.596A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.548A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.527A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.712A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.455A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.116A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.493A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.969A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.658A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.658A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.849A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.849A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.596A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.548A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.527A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.215A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.116A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.492A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.456A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.968A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.718A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.718A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 1142 hydrogen bonds defined for protein. 3138 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: 7.31 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 6100 1.33 - 1.47: 9351 1.47 - 1.61: 11481 1.61 - 1.76: 8 1.76 - 1.90: 136 Bond restraints: 27076 Sorted by residual: bond pdb=" CG ASN C 709 " pdb=" ND2 ASN C 709 " ideal model delta sigma weight residual 1.328 1.513 -0.185 2.10e-02 2.27e+03 7.80e+01 bond pdb=" CG ASN B 709 " pdb=" ND2 ASN B 709 " ideal model delta sigma weight residual 1.328 1.511 -0.183 2.10e-02 2.27e+03 7.57e+01 bond pdb=" CG ASN A 709 " pdb=" ND2 ASN A 709 " ideal model delta sigma weight residual 1.328 1.511 -0.183 2.10e-02 2.27e+03 7.56e+01 bond pdb=" C ELA A1606 " pdb=" OXT ELA A1606 " ideal model delta sigma weight residual 1.250 1.404 -0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" C ELA A1607 " pdb=" OXT ELA A1607 " ideal model delta sigma weight residual 1.250 1.403 -0.153 2.00e-02 2.50e+03 5.84e+01 ... (remaining 27071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 35765 2.62 - 5.24: 927 5.24 - 7.86: 102 7.86 - 10.48: 19 10.48 - 13.10: 2 Bond angle restraints: 36815 Sorted by residual: angle pdb=" N ARG C 319 " pdb=" CA ARG C 319 " pdb=" C ARG C 319 " ideal model delta sigma weight residual 111.28 120.77 -9.49 1.09e+00 8.42e-01 7.58e+01 angle pdb=" N THR A 167 " pdb=" CA THR A 167 " pdb=" C THR A 167 " ideal model delta sigma weight residual 111.36 120.48 -9.12 1.09e+00 8.42e-01 6.99e+01 angle pdb=" N ASN B 616 " pdb=" CA ASN B 616 " pdb=" C ASN B 616 " ideal model delta sigma weight residual 109.85 96.75 13.10 1.58e+00 4.01e-01 6.87e+01 angle pdb=" N THR B 167 " pdb=" CA THR B 167 " pdb=" C THR B 167 " ideal model delta sigma weight residual 111.36 120.01 -8.65 1.09e+00 8.42e-01 6.29e+01 angle pdb=" N LYS A 835 " pdb=" CA LYS A 835 " pdb=" C LYS A 835 " ideal model delta sigma weight residual 110.10 99.09 11.01 1.49e+00 4.50e-01 5.46e+01 ... (remaining 36810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15527 17.99 - 35.98: 1227 35.98 - 53.98: 342 53.98 - 71.97: 84 71.97 - 89.96: 31 Dihedral angle restraints: 17211 sinusoidal: 7779 harmonic: 9432 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -173.44 87.44 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.43 78.43 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.41 78.41 1 1.00e+01 1.00e-02 7.67e+01 ... (remaining 17208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.332: 4394 0.332 - 0.664: 17 0.664 - 0.995: 8 0.995 - 1.327: 1 1.327 - 1.659: 3 Chirality restraints: 4423 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.88e+03 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.87e+03 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.87e+03 ... (remaining 4420 not shown) Planarity restraints: 4703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.329 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG D 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1607 " -0.323 2.00e-02 2.50e+03 2.80e-01 9.83e+02 pdb=" C7 NAG B1607 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1607 " -0.132 2.00e-02 2.50e+03 pdb=" N2 NAG B1607 " 0.502 2.00e-02 2.50e+03 pdb=" O7 NAG B1607 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1606 " -0.321 2.00e-02 2.50e+03 2.78e-01 9.68e+02 pdb=" C7 NAG C1606 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG C1606 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG C1606 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG C1606 " -0.117 2.00e-02 2.50e+03 ... (remaining 4700 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 897 2.69 - 3.24: 25285 3.24 - 3.80: 41610 3.80 - 4.35: 55464 4.35 - 4.90: 94065 Nonbonded interactions: 217321 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.140 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.140 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.141 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.218 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.218 3.040 ... (remaining 217316 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 1147 or resid 1602 through 1605)) selection = (chain 'B' and (resid 14 through 1147 or resid 1602 through 1605)) selection = (chain 'C' and (resid 14 through 1147 or resid 1602 through 1605)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 25.530 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.185 27201 Z= 0.462 Angle : 1.302 34.242 37148 Z= 0.666 Chirality : 0.090 1.659 4423 Planarity : 0.013 0.286 4652 Dihedral : 14.427 89.962 11013 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.69 % Allowed : 5.64 % Favored : 90.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.13), residues: 3198 helix: -1.40 (0.15), residues: 768 sheet: 0.15 (0.19), residues: 714 loop : -1.64 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 190 TYR 0.040 0.002 TYR B 756 PHE 0.019 0.002 PHE A 43 TRP 0.052 0.004 TRP A 886 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00933 (27076) covalent geometry : angle 1.02307 (36815) SS BOND : bond 0.00742 ( 42) SS BOND : angle 3.10081 ( 84) hydrogen bonds : bond 0.13506 ( 1091) hydrogen bonds : angle 7.63732 ( 3138) link_BETA1-4 : bond 0.05676 ( 32) link_BETA1-4 : angle 12.41614 ( 96) link_NAG-ASN : bond 0.00990 ( 51) link_NAG-ASN : angle 7.59233 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 364 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 319 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6413 (ptt-90) REVERT: A 487 ASN cc_start: 0.7045 (m110) cc_final: 0.6797 (m-40) REVERT: A 613 GLN cc_start: 0.7222 (pm20) cc_final: 0.6695 (tt0) REVERT: A 630 THR cc_start: 0.6614 (OUTLIER) cc_final: 0.5691 (p) REVERT: A 634 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7867 (ttm110) REVERT: A 814 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7930 (mmpt) REVERT: A 836 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6531 (pt0) REVERT: A 902 MET cc_start: 0.8629 (mmm) cc_final: 0.8317 (tpt) REVERT: A 1028 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8882 (mttm) REVERT: A 1029 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8761 (ttp) REVERT: B 287 ASP cc_start: 0.7918 (t0) cc_final: 0.7713 (t0) REVERT: B 319 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6356 (ptt-90) REVERT: B 487 ASN cc_start: 0.6982 (m110) cc_final: 0.6691 (m-40) REVERT: B 747 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8757 (p) REVERT: B 787 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7640 (mm-40) REVERT: B 814 LYS cc_start: 0.8376 (mtpt) cc_final: 0.7951 (mmpt) REVERT: C 30 ASN cc_start: 0.7004 (m110) cc_final: 0.6658 (t0) REVERT: C 321 GLN cc_start: 0.7023 (mp10) cc_final: 0.6789 (mp10) REVERT: C 606 ASN cc_start: 0.8555 (m110) cc_final: 0.8066 (t0) REVERT: C 629 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7364 (mt) REVERT: C 630 THR cc_start: 0.7442 (OUTLIER) cc_final: 0.6906 (p) REVERT: C 814 LYS cc_start: 0.8343 (mtpt) cc_final: 0.7911 (mmpt) REVERT: C 902 MET cc_start: 0.8742 (mmm) cc_final: 0.8402 (mmm) REVERT: C 1028 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8934 (mttm) REVERT: C 1092 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8068 (mm-30) outliers start: 104 outliers final: 30 residues processed: 440 average time/residue: 0.1703 time to fit residues: 117.7204 Evaluate side-chains 232 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 134 GLN A 239 GLN A 481 ASN A 487 ASN A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 901 GLN A 926 GLN A1005 GLN B 115 GLN B 121 ASN B 134 GLN B 239 GLN B 314 GLN B 487 ASN B 580 GLN B 607 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 901 GLN B 926 GLN B1005 GLN C 30 ASN C 121 ASN C 134 GLN C 211 ASN C 314 GLN C 474 GLN C 481 ASN C 487 ASN C 493 GLN C 498 GLN C 580 GLN C 606 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 901 GLN C 926 GLN C1005 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100615 restraints weight = 40249.109| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.75 r_work: 0.3130 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27201 Z= 0.144 Angle : 0.695 19.062 37148 Z= 0.335 Chirality : 0.047 0.384 4423 Planarity : 0.005 0.049 4652 Dihedral : 8.851 80.309 5338 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.31 % Allowed : 8.84 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3198 helix: 0.54 (0.18), residues: 768 sheet: 0.25 (0.19), residues: 756 loop : -1.36 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 158 TYR 0.019 0.001 TYR B 756 PHE 0.013 0.001 PHE C 318 TRP 0.020 0.002 TRP C 886 HIS 0.002 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00319 (27076) covalent geometry : angle 0.61224 (36815) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.89446 ( 84) hydrogen bonds : bond 0.04731 ( 1091) hydrogen bonds : angle 5.92247 ( 3138) link_BETA1-4 : bond 0.00307 ( 32) link_BETA1-4 : angle 2.56531 ( 96) link_NAG-ASN : bond 0.00646 ( 51) link_NAG-ASN : angle 4.56482 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 234 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6370 (p0) cc_final: 0.6005 (p0) REVERT: A 88 ASP cc_start: 0.8207 (p0) cc_final: 0.8000 (p0) REVERT: A 144 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.6014 (m-80) REVERT: A 613 GLN cc_start: 0.7368 (pm20) cc_final: 0.6791 (tt0) REVERT: A 814 LYS cc_start: 0.8556 (mtpt) cc_final: 0.7899 (mmpt) REVERT: A 1050 MET cc_start: 0.9004 (ptp) cc_final: 0.8655 (ptp) REVERT: B 49 HIS cc_start: 0.7408 (t70) cc_final: 0.6961 (m90) REVERT: B 287 ASP cc_start: 0.8434 (t0) cc_final: 0.8030 (t0) REVERT: B 814 LYS cc_start: 0.8484 (mtpt) cc_final: 0.7810 (mmpt) REVERT: B 902 MET cc_start: 0.8635 (tpt) cc_final: 0.8353 (tpt) REVERT: C 30 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7104 (t0) REVERT: C 81 ASN cc_start: 0.6209 (p0) cc_final: 0.5913 (p0) REVERT: C 287 ASP cc_start: 0.8429 (t0) cc_final: 0.8034 (t0) REVERT: C 487 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7197 (t0) REVERT: C 529 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7494 (mmtt) REVERT: C 606 ASN cc_start: 0.8781 (m-40) cc_final: 0.8034 (t0) REVERT: C 630 THR cc_start: 0.7010 (OUTLIER) cc_final: 0.6807 (p) REVERT: C 814 LYS cc_start: 0.8587 (mtpt) cc_final: 0.7878 (mmpt) REVERT: C 878 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8414 (mm) REVERT: C 902 MET cc_start: 0.8875 (mmm) cc_final: 0.8601 (mmm) REVERT: C 1073 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8143 (mmtp) outliers start: 65 outliers final: 27 residues processed: 287 average time/residue: 0.1494 time to fit residues: 71.0492 Evaluate side-chains 213 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 280 ASN B 628 GLN B 804 GLN B1142 GLN C 121 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 955 ASN C 965 GLN C1142 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095797 restraints weight = 40807.498| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.78 r_work: 0.3048 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 27201 Z= 0.236 Angle : 0.706 17.773 37148 Z= 0.344 Chirality : 0.048 0.327 4423 Planarity : 0.005 0.043 4652 Dihedral : 8.087 80.710 5274 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.38 % Allowed : 10.54 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3198 helix: 1.11 (0.19), residues: 747 sheet: 0.39 (0.19), residues: 732 loop : -1.31 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1107 TYR 0.031 0.002 TYR B 756 PHE 0.017 0.002 PHE A 133 TRP 0.020 0.002 TRP C 886 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00563 (27076) covalent geometry : angle 0.64223 (36815) SS BOND : bond 0.01069 ( 42) SS BOND : angle 2.78552 ( 84) hydrogen bonds : bond 0.04881 ( 1091) hydrogen bonds : angle 5.68681 ( 3138) link_BETA1-4 : bond 0.00424 ( 32) link_BETA1-4 : angle 2.30877 ( 96) link_NAG-ASN : bond 0.00702 ( 51) link_NAG-ASN : angle 3.77296 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 195 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6373 (p0) cc_final: 0.5975 (p0) REVERT: A 242 LEU cc_start: 0.8008 (mt) cc_final: 0.7794 (mt) REVERT: A 585 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6306 (tp) REVERT: A 814 LYS cc_start: 0.8496 (mtpt) cc_final: 0.7875 (mmpt) REVERT: A 1028 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9024 (tttt) REVERT: B 49 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6840 (m-70) REVERT: B 138 ASP cc_start: 0.8411 (m-30) cc_final: 0.8166 (m-30) REVERT: B 287 ASP cc_start: 0.8245 (t0) cc_final: 0.7868 (t0) REVERT: B 443 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8184 (p) REVERT: B 814 LYS cc_start: 0.8434 (mtpt) cc_final: 0.7781 (mmpt) REVERT: B 902 MET cc_start: 0.8719 (tpt) cc_final: 0.8475 (tpt) REVERT: C 30 ASN cc_start: 0.7619 (m-40) cc_final: 0.7159 (t0) REVERT: C 49 HIS cc_start: 0.7148 (t70) cc_final: 0.6921 (t70) REVERT: C 54 LEU cc_start: 0.8547 (mt) cc_final: 0.8335 (mt) REVERT: C 81 ASN cc_start: 0.6419 (p0) cc_final: 0.6110 (p0) REVERT: C 287 ASP cc_start: 0.8415 (t0) cc_final: 0.7773 (t0) REVERT: C 487 ASN cc_start: 0.7862 (t0) cc_final: 0.7476 (t0) REVERT: C 606 ASN cc_start: 0.8761 (m-40) cc_final: 0.8148 (t0) REVERT: C 613 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.6929 (tt0) REVERT: C 814 LYS cc_start: 0.8567 (mtpt) cc_final: 0.7870 (mmpt) REVERT: C 878 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8413 (mm) REVERT: C 988 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8305 (mt-10) outliers start: 67 outliers final: 44 residues processed: 250 average time/residue: 0.1477 time to fit residues: 61.9047 Evaluate side-chains 210 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 164 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 247 optimal weight: 0.0270 chunk 38 optimal weight: 0.0770 chunk 167 optimal weight: 0.8980 chunk 314 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 115 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101517 restraints weight = 40317.976| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.02 r_work: 0.3082 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 27201 Z= 0.109 Angle : 0.603 16.795 37148 Z= 0.292 Chirality : 0.045 0.290 4423 Planarity : 0.004 0.041 4652 Dihedral : 7.582 80.555 5270 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.70 % Allowed : 11.54 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3198 helix: 1.66 (0.20), residues: 735 sheet: 0.53 (0.19), residues: 729 loop : -1.15 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 158 TYR 0.017 0.001 TYR C1067 PHE 0.012 0.001 PHE B 318 TRP 0.010 0.001 TRP C 886 HIS 0.005 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00237 (27076) covalent geometry : angle 0.54440 (36815) SS BOND : bond 0.00388 ( 42) SS BOND : angle 2.18178 ( 84) hydrogen bonds : bond 0.03836 ( 1091) hydrogen bonds : angle 5.35834 ( 3138) link_BETA1-4 : bond 0.00368 ( 32) link_BETA1-4 : angle 1.99146 ( 96) link_NAG-ASN : bond 0.00554 ( 51) link_NAG-ASN : angle 3.44416 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6272 (p0) cc_final: 0.5865 (p0) REVERT: A 606 ASN cc_start: 0.8525 (m-40) cc_final: 0.7331 (t0) REVERT: A 613 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6881 (tt0) REVERT: A 814 LYS cc_start: 0.8476 (mtpt) cc_final: 0.7849 (mmpt) REVERT: A 1073 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8093 (mmtp) REVERT: B 138 ASP cc_start: 0.8507 (m-30) cc_final: 0.8270 (m-30) REVERT: B 287 ASP cc_start: 0.8251 (t0) cc_final: 0.7901 (t0) REVERT: B 443 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8028 (p) REVERT: B 582 LEU cc_start: 0.8052 (mm) cc_final: 0.7195 (tp) REVERT: B 606 ASN cc_start: 0.8705 (m-40) cc_final: 0.7301 (t0) REVERT: B 814 LYS cc_start: 0.8453 (mtpt) cc_final: 0.7802 (mmpt) REVERT: B 902 MET cc_start: 0.8666 (tpt) cc_final: 0.8418 (tpt) REVERT: B 988 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7925 (mt-10) REVERT: C 30 ASN cc_start: 0.7442 (m-40) cc_final: 0.6989 (t0) REVERT: C 81 ASN cc_start: 0.6335 (p0) cc_final: 0.6099 (p0) REVERT: C 200 TYR cc_start: 0.8089 (m-80) cc_final: 0.7812 (m-80) REVERT: C 287 ASP cc_start: 0.8495 (t0) cc_final: 0.7835 (t0) REVERT: C 606 ASN cc_start: 0.8623 (m-40) cc_final: 0.7897 (t0) REVERT: C 613 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: C 814 LYS cc_start: 0.8565 (mtpt) cc_final: 0.7864 (mmpt) REVERT: C 878 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8420 (mm) REVERT: C 988 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8254 (mt-10) REVERT: C 1073 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8181 (mmtp) outliers start: 48 outliers final: 28 residues processed: 233 average time/residue: 0.1446 time to fit residues: 56.7258 Evaluate side-chains 198 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 18 optimal weight: 0.0000 chunk 184 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 200 optimal weight: 0.5980 chunk 295 optimal weight: 0.4980 chunk 242 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS A 121 ASN B 69 HIS B1119 ASN C 30 ASN C 115 GLN C 121 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096637 restraints weight = 40291.691| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.58 r_work: 0.3102 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27201 Z= 0.143 Angle : 0.597 16.251 37148 Z= 0.289 Chirality : 0.045 0.297 4423 Planarity : 0.004 0.042 4652 Dihedral : 7.375 80.382 5267 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.06 % Allowed : 11.57 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3198 helix: 1.76 (0.20), residues: 735 sheet: 0.49 (0.19), residues: 726 loop : -1.12 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.019 0.001 TYR B 756 PHE 0.010 0.001 PHE C 133 TRP 0.012 0.001 TRP C 886 HIS 0.013 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00335 (27076) covalent geometry : angle 0.54398 (36815) SS BOND : bond 0.00289 ( 42) SS BOND : angle 1.84504 ( 84) hydrogen bonds : bond 0.03952 ( 1091) hydrogen bonds : angle 5.27304 ( 3138) link_BETA1-4 : bond 0.00333 ( 32) link_BETA1-4 : angle 1.96024 ( 96) link_NAG-ASN : bond 0.00509 ( 51) link_NAG-ASN : angle 3.31958 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.880 Fit side-chains REVERT: A 606 ASN cc_start: 0.8583 (m-40) cc_final: 0.7406 (t0) REVERT: A 613 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.6946 (tt0) REVERT: A 814 LYS cc_start: 0.8535 (mtpt) cc_final: 0.7858 (mmpt) REVERT: A 1028 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.8984 (mttm) REVERT: A 1073 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8217 (mmtp) REVERT: B 138 ASP cc_start: 0.8616 (m-30) cc_final: 0.8374 (m-30) REVERT: B 287 ASP cc_start: 0.8320 (t0) cc_final: 0.7988 (t0) REVERT: B 443 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8121 (p) REVERT: B 582 LEU cc_start: 0.8079 (mm) cc_final: 0.7205 (tp) REVERT: B 606 ASN cc_start: 0.8793 (m-40) cc_final: 0.7430 (t0) REVERT: B 814 LYS cc_start: 0.8508 (mtpt) cc_final: 0.7820 (mmpt) REVERT: B 902 MET cc_start: 0.8721 (tpt) cc_final: 0.8478 (tpt) REVERT: B 988 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8031 (mt-10) REVERT: C 30 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7083 (t0) REVERT: C 54 LEU cc_start: 0.8499 (mt) cc_final: 0.8246 (mt) REVERT: C 200 TYR cc_start: 0.8210 (m-80) cc_final: 0.7906 (m-80) REVERT: C 287 ASP cc_start: 0.8625 (t0) cc_final: 0.7995 (t0) REVERT: C 580 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: C 606 ASN cc_start: 0.8709 (m-40) cc_final: 0.7963 (t0) REVERT: C 613 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7019 (tt0) REVERT: C 814 LYS cc_start: 0.8610 (mtpt) cc_final: 0.7873 (mmpt) REVERT: C 878 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8589 (mm) REVERT: C 988 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8356 (mt-10) REVERT: C 1073 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8255 (mmtp) outliers start: 58 outliers final: 38 residues processed: 225 average time/residue: 0.1479 time to fit residues: 55.4969 Evaluate side-chains 207 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 323 optimal weight: 0.0070 chunk 176 optimal weight: 0.8980 chunk 260 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN C 121 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095315 restraints weight = 40679.220| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.61 r_work: 0.3077 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27201 Z= 0.191 Angle : 0.620 15.872 37148 Z= 0.301 Chirality : 0.046 0.299 4423 Planarity : 0.004 0.044 4652 Dihedral : 7.353 80.565 5266 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.56 % Allowed : 11.71 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3198 helix: 1.74 (0.20), residues: 735 sheet: 0.46 (0.19), residues: 723 loop : -1.15 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 466 TYR 0.025 0.001 TYR B 756 PHE 0.012 0.001 PHE C 133 TRP 0.015 0.002 TRP C 886 HIS 0.010 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00458 (27076) covalent geometry : angle 0.56995 (36815) SS BOND : bond 0.00353 ( 42) SS BOND : angle 1.87421 ( 84) hydrogen bonds : bond 0.04258 ( 1091) hydrogen bonds : angle 5.31179 ( 3138) link_BETA1-4 : bond 0.00357 ( 32) link_BETA1-4 : angle 1.92717 ( 96) link_NAG-ASN : bond 0.00510 ( 51) link_NAG-ASN : angle 3.31097 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 166 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 606 ASN cc_start: 0.8710 (m-40) cc_final: 0.7515 (t0) REVERT: A 613 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: A 814 LYS cc_start: 0.8566 (mtpt) cc_final: 0.7832 (mmpt) REVERT: A 837 TYR cc_start: 0.6506 (t80) cc_final: 0.6236 (t80) REVERT: A 1028 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.8947 (mttm) REVERT: A 1073 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8205 (mmtp) REVERT: B 138 ASP cc_start: 0.8630 (m-30) cc_final: 0.8382 (m-30) REVERT: B 287 ASP cc_start: 0.8364 (t0) cc_final: 0.8046 (t0) REVERT: B 443 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 582 LEU cc_start: 0.7995 (mm) cc_final: 0.7091 (tp) REVERT: B 606 ASN cc_start: 0.8761 (m-40) cc_final: 0.7554 (t0) REVERT: B 814 LYS cc_start: 0.8517 (mtpt) cc_final: 0.7748 (mmpt) REVERT: B 988 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7994 (mt-10) REVERT: C 200 TYR cc_start: 0.8222 (m-80) cc_final: 0.7919 (m-80) REVERT: C 287 ASP cc_start: 0.8652 (t0) cc_final: 0.8019 (t0) REVERT: C 580 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7020 (mt0) REVERT: C 606 ASN cc_start: 0.8800 (m-40) cc_final: 0.8049 (t0) REVERT: C 613 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: C 814 LYS cc_start: 0.8648 (mtpt) cc_final: 0.7854 (mmpt) REVERT: C 878 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8610 (mm) REVERT: C 964 LYS cc_start: 0.9148 (tttt) cc_final: 0.8928 (ttmt) REVERT: C 988 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8353 (mt-10) outliers start: 72 outliers final: 51 residues processed: 227 average time/residue: 0.1431 time to fit residues: 55.3404 Evaluate side-chains 215 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 158 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 285 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 181 optimal weight: 0.0980 chunk 176 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN C 121 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095151 restraints weight = 40475.849| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.75 r_work: 0.3067 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27201 Z= 0.182 Angle : 0.608 15.568 37148 Z= 0.295 Chirality : 0.045 0.292 4423 Planarity : 0.004 0.044 4652 Dihedral : 7.209 77.624 5266 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.31 % Allowed : 12.53 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3198 helix: 1.78 (0.20), residues: 735 sheet: 0.44 (0.19), residues: 720 loop : -1.18 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.024 0.001 TYR B 756 PHE 0.011 0.001 PHE C 133 TRP 0.015 0.001 TRP C 886 HIS 0.010 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00436 (27076) covalent geometry : angle 0.55917 (36815) SS BOND : bond 0.00327 ( 42) SS BOND : angle 1.80197 ( 84) hydrogen bonds : bond 0.04211 ( 1091) hydrogen bonds : angle 5.27663 ( 3138) link_BETA1-4 : bond 0.00360 ( 32) link_BETA1-4 : angle 1.88790 ( 96) link_NAG-ASN : bond 0.00494 ( 51) link_NAG-ASN : angle 3.24721 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 167 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 606 ASN cc_start: 0.8707 (m-40) cc_final: 0.7545 (t0) REVERT: A 613 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: A 814 LYS cc_start: 0.8645 (mtpt) cc_final: 0.7802 (mmpt) REVERT: A 1028 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.8974 (mttm) REVERT: A 1073 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8220 (mmtp) REVERT: B 138 ASP cc_start: 0.8643 (m-30) cc_final: 0.8393 (m-30) REVERT: B 287 ASP cc_start: 0.8355 (t0) cc_final: 0.8030 (t0) REVERT: B 443 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8127 (p) REVERT: B 582 LEU cc_start: 0.7993 (mm) cc_final: 0.7032 (tp) REVERT: B 606 ASN cc_start: 0.8801 (m-40) cc_final: 0.7622 (t0) REVERT: B 814 LYS cc_start: 0.8558 (mtpt) cc_final: 0.7715 (mmpt) REVERT: B 988 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8034 (mt-10) REVERT: C 200 TYR cc_start: 0.8180 (m-80) cc_final: 0.7892 (m-80) REVERT: C 287 ASP cc_start: 0.8640 (t0) cc_final: 0.8022 (t0) REVERT: C 580 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7004 (mt0) REVERT: C 606 ASN cc_start: 0.8806 (m-40) cc_final: 0.8141 (t0) REVERT: C 613 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: C 878 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8659 (mm) REVERT: C 964 LYS cc_start: 0.9142 (tttt) cc_final: 0.8925 (ttmt) REVERT: C 988 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8331 (mt-10) outliers start: 65 outliers final: 52 residues processed: 220 average time/residue: 0.1417 time to fit residues: 53.0668 Evaluate side-chains 220 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 62 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 314 optimal weight: 0.6980 chunk 251 optimal weight: 0.6980 chunk 179 optimal weight: 0.0050 chunk 167 optimal weight: 2.9990 chunk 311 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 154 optimal weight: 0.0470 chunk 42 optimal weight: 0.0030 overall best weight: 0.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS A 913 GLN B 764 ASN B 913 GLN C 115 GLN C 121 ASN ** C 613 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 = 0.3795 r_free = 0.3795 target = 0.135662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.098369 restraints weight = 40305.682| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.61 r_work: 0.3128 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27201 Z= 0.096 Angle : 0.551 14.849 37148 Z= 0.268 Chirality : 0.044 0.266 4423 Planarity : 0.004 0.044 4652 Dihedral : 6.749 72.210 5266 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.63 % Allowed : 13.38 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3198 helix: 2.07 (0.20), residues: 735 sheet: 0.59 (0.19), residues: 729 loop : -1.08 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 158 TYR 0.018 0.001 TYR B1067 PHE 0.011 0.001 PHE C 318 TRP 0.010 0.001 TRP C 886 HIS 0.011 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00207 (27076) covalent geometry : angle 0.50576 (36815) SS BOND : bond 0.00344 ( 42) SS BOND : angle 1.24077 ( 84) hydrogen bonds : bond 0.03440 ( 1091) hydrogen bonds : angle 5.04424 ( 3138) link_BETA1-4 : bond 0.00434 ( 32) link_BETA1-4 : angle 1.76506 ( 96) link_NAG-ASN : bond 0.00435 ( 51) link_NAG-ASN : angle 3.05000 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8084 (p0) cc_final: 0.7855 (p0) REVERT: A 606 ASN cc_start: 0.8582 (m-40) cc_final: 0.7449 (t0) REVERT: A 613 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: A 814 LYS cc_start: 0.8629 (mtpt) cc_final: 0.7780 (mmpt) REVERT: A 1073 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8206 (mmtp) REVERT: B 138 ASP cc_start: 0.8644 (m-30) cc_final: 0.8406 (m-30) REVERT: B 287 ASP cc_start: 0.8245 (t0) cc_final: 0.7953 (t0) REVERT: B 443 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8013 (p) REVERT: B 582 LEU cc_start: 0.8030 (mm) cc_final: 0.7147 (tp) REVERT: B 606 ASN cc_start: 0.8717 (m-40) cc_final: 0.7479 (t0) REVERT: B 814 LYS cc_start: 0.8586 (mtpt) cc_final: 0.7780 (mmpt) REVERT: B 988 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8034 (mt-10) REVERT: C 200 TYR cc_start: 0.8094 (m-80) cc_final: 0.7869 (m-80) REVERT: C 287 ASP cc_start: 0.8560 (t0) cc_final: 0.7964 (t0) REVERT: C 580 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6952 (mt0) REVERT: C 606 ASN cc_start: 0.8692 (m-40) cc_final: 0.7933 (t0) REVERT: C 902 MET cc_start: 0.8950 (tpp) cc_final: 0.8622 (mmm) REVERT: C 988 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 1073 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8239 (mmtp) outliers start: 46 outliers final: 32 residues processed: 234 average time/residue: 0.1502 time to fit residues: 58.7509 Evaluate side-chains 209 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 295 optimal weight: 0.0050 chunk 145 optimal weight: 0.9980 chunk 111 optimal weight: 0.0070 chunk 13 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 overall best weight: 0.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS B1119 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097588 restraints weight = 41070.582| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.63 r_work: 0.3122 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27201 Z= 0.114 Angle : 0.560 14.509 37148 Z= 0.272 Chirality : 0.044 0.276 4423 Planarity : 0.004 0.052 4652 Dihedral : 6.656 69.864 5266 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.35 % Allowed : 13.99 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3198 helix: 2.15 (0.20), residues: 735 sheet: 0.55 (0.19), residues: 741 loop : -1.04 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 190 TYR 0.017 0.001 TYR C1067 PHE 0.011 0.001 PHE C 220 TRP 0.011 0.001 TRP C 886 HIS 0.011 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00261 (27076) covalent geometry : angle 0.51732 (36815) SS BOND : bond 0.00409 ( 42) SS BOND : angle 1.36304 ( 84) hydrogen bonds : bond 0.03549 ( 1091) hydrogen bonds : angle 5.03511 ( 3138) link_BETA1-4 : bond 0.00355 ( 32) link_BETA1-4 : angle 1.74322 ( 96) link_NAG-ASN : bond 0.00404 ( 51) link_NAG-ASN : angle 2.97023 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 556 ASN cc_start: 0.8168 (m-40) cc_final: 0.7191 (p0) REVERT: A 606 ASN cc_start: 0.8594 (m-40) cc_final: 0.7476 (t0) REVERT: A 613 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: A 814 LYS cc_start: 0.8624 (mtpt) cc_final: 0.7806 (mmpt) REVERT: A 1073 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8151 (mmtp) REVERT: B 138 ASP cc_start: 0.8675 (m-30) cc_final: 0.8430 (m-30) REVERT: B 287 ASP cc_start: 0.8312 (t0) cc_final: 0.8008 (t0) REVERT: B 443 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8099 (p) REVERT: B 582 LEU cc_start: 0.8018 (mm) cc_final: 0.7082 (tp) REVERT: B 606 ASN cc_start: 0.8720 (m-40) cc_final: 0.7507 (t0) REVERT: B 814 LYS cc_start: 0.8538 (mtpt) cc_final: 0.7772 (mmpt) REVERT: B 988 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8113 (mt-10) REVERT: C 200 TYR cc_start: 0.8182 (m-80) cc_final: 0.7970 (m-80) REVERT: C 287 ASP cc_start: 0.8606 (t0) cc_final: 0.7933 (t0) REVERT: C 487 ASN cc_start: 0.7694 (m-40) cc_final: 0.7248 (t0) REVERT: C 606 ASN cc_start: 0.8617 (m-40) cc_final: 0.7903 (t0) REVERT: C 902 MET cc_start: 0.8983 (tpp) cc_final: 0.8511 (mmm) REVERT: C 964 LYS cc_start: 0.9135 (tttt) cc_final: 0.8916 (ttmt) REVERT: C 988 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8364 (mt-10) REVERT: C 1073 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8261 (mmtp) outliers start: 38 outliers final: 30 residues processed: 207 average time/residue: 0.1434 time to fit residues: 50.0462 Evaluate side-chains 204 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 120 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 313 optimal weight: 0.0980 chunk 109 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 176 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B1119 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096909 restraints weight = 40297.420| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.55 r_work: 0.3100 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27201 Z= 0.138 Angle : 0.569 14.164 37148 Z= 0.277 Chirality : 0.044 0.283 4423 Planarity : 0.004 0.047 4652 Dihedral : 6.663 68.687 5265 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.17 % Allowed : 14.34 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3198 helix: 1.94 (0.20), residues: 759 sheet: 0.55 (0.19), residues: 735 loop : -1.08 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.017 0.001 TYR B 756 PHE 0.010 0.001 PHE C1121 TRP 0.015 0.001 TRP C 886 HIS 0.010 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00324 (27076) covalent geometry : angle 0.52768 (36815) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.50473 ( 84) hydrogen bonds : bond 0.03824 ( 1091) hydrogen bonds : angle 5.08625 ( 3138) link_BETA1-4 : bond 0.00335 ( 32) link_BETA1-4 : angle 1.72824 ( 96) link_NAG-ASN : bond 0.00390 ( 51) link_NAG-ASN : angle 2.93279 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 556 ASN cc_start: 0.8216 (m-40) cc_final: 0.7177 (p0) REVERT: A 606 ASN cc_start: 0.8627 (m-40) cc_final: 0.7561 (t0) REVERT: A 613 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: A 814 LYS cc_start: 0.8622 (mtpt) cc_final: 0.7781 (mmpt) REVERT: A 1073 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8163 (mmtp) REVERT: B 138 ASP cc_start: 0.8632 (m-30) cc_final: 0.8388 (m-30) REVERT: B 287 ASP cc_start: 0.8313 (t0) cc_final: 0.8021 (t0) REVERT: B 443 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8094 (p) REVERT: B 582 LEU cc_start: 0.7956 (mm) cc_final: 0.7012 (tp) REVERT: B 606 ASN cc_start: 0.8728 (m-40) cc_final: 0.7519 (t0) REVERT: B 814 LYS cc_start: 0.8611 (mtpt) cc_final: 0.7805 (mmpt) REVERT: B 988 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7972 (mt-10) REVERT: C 200 TYR cc_start: 0.8092 (m-80) cc_final: 0.7868 (m-80) REVERT: C 287 ASP cc_start: 0.8572 (t0) cc_final: 0.7980 (t0) REVERT: C 487 ASN cc_start: 0.7764 (m-40) cc_final: 0.7314 (t0) REVERT: C 580 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6961 (mt0) REVERT: C 606 ASN cc_start: 0.8758 (m-40) cc_final: 0.8041 (t0) REVERT: C 902 MET cc_start: 0.8941 (tpp) cc_final: 0.8474 (mmm) REVERT: C 964 LYS cc_start: 0.9131 (tttt) cc_final: 0.8916 (ttmt) REVERT: C 988 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8304 (mt-10) outliers start: 33 outliers final: 28 residues processed: 201 average time/residue: 0.1458 time to fit residues: 49.4228 Evaluate side-chains 203 residues out of total 2817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 125 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 251 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 314 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 312 optimal weight: 0.6980 chunk 274 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS C 121 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101912 restraints weight = 40681.533| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.97 r_work: 0.3091 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27201 Z= 0.102 Angle : 0.542 14.906 37148 Z= 0.264 Chirality : 0.043 0.266 4423 Planarity : 0.004 0.044 4652 Dihedral : 6.463 61.722 5265 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.31 % Allowed : 14.38 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3198 helix: 2.12 (0.20), residues: 756 sheet: 0.47 (0.19), residues: 705 loop : -0.92 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.017 0.001 TYR B1067 PHE 0.010 0.001 PHE C 318 TRP 0.010 0.001 TRP C 886 HIS 0.011 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00229 (27076) covalent geometry : angle 0.50036 (36815) SS BOND : bond 0.00317 ( 42) SS BOND : angle 1.26147 ( 84) hydrogen bonds : bond 0.03435 ( 1091) hydrogen bonds : angle 4.97163 ( 3138) link_BETA1-4 : bond 0.00367 ( 32) link_BETA1-4 : angle 1.66942 ( 96) link_NAG-ASN : bond 0.00374 ( 51) link_NAG-ASN : angle 2.88643 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6442.06 seconds wall clock time: 110 minutes 59.79 seconds (6659.79 seconds total)