Starting phenix.real_space_refine on Fri Mar 6 05:58:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swx_25488/03_2026/7swx_25488.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swx_25488/03_2026/7swx_25488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7swx_25488/03_2026/7swx_25488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swx_25488/03_2026/7swx_25488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7swx_25488/03_2026/7swx_25488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swx_25488/03_2026/7swx_25488.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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 125 5.16 5 C 18208 2.51 5 N 4674 2.21 5 O 5662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 28669 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8557 Classifications: {'peptide': 1095} Link IDs: {'PTRANS': 56, 'TRANS': 1038} Chain breaks: 4 Chain: "B" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 916 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 106} 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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.89, per 1000 atoms: 0.24 Number of scatterers: 28669 At special positions: 0 Unit cell: (154, 171.6, 183.7, 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 125 16.00 O 5662 8.00 N 4674 7.00 C 18208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1401 " - " ASN A 17 " " NAG A1402 " - " ASN A 61 " " NAG A1403 " - " ASN A 125 " " NAG A1404 " - " ASN A 149 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 149 " " NAG B1204 " - " ASN B 165 " " NAG B1205 " - " ASN B 234 " " NAG B1206 " - " ASN B 282 " " NAG B1207 " - " ASN B 603 " " NAG B1208 " - " ASN B 657 " " NAG B1209 " - " ASN B 709 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 149 " " NAG C1204 " - " ASN C 165 " " NAG C1205 " - " ASN C 234 " " NAG C1206 " - " ASN C 282 " " NAG C1207 " - " ASN C 603 " " NAG C1208 " - " ASN C 657 " " NAG C1209 " - " ASN C 709 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 616 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 17 " " NAG S 1 " - " ASN C 616 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1134 " " NAG W 1 " - " ASN A 331 " " NAG X 1 " - " ASN A 717 " " NAG Y 1 " - " ASN A1074 " " NAG Z 1 " - " ASN A1098 " " NAG a 1 " - " ASN B 717 " " NAG b 1 " - " ASN B1098 " " NAG c 1 " - " ASN C 331 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN B 331 " " NAG g 1 " - " ASN C 343 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6570 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 52 sheets defined 22.1% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.518A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.726A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.536A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.535A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.518A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.658A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.256A 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 removed outlier: 4.075A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.504A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.679A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.636A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.660A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.577A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.583A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.539A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.598A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.359A 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 removed outlier: 3.798A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.927A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.522A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.827A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.658A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.530A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.619A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.538A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.738A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.582A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.358A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.119A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.859A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'H' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.468A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.517A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.881A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.536A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.070A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.789A 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 315 removed outlier: 4.633A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.258A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.401A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (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 654 through 660 removed outlier: 6.391A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.332A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.332A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.416A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.197A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.517A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.784A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.784A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.428A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.554A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.540A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.009A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.516A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.516A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.530A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.997A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.997A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.253A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.007A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.916A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.278A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.493A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.386A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.386A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.583A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.553A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.913A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.543A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.141A pdb=" N CYS H 96 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRP H 108 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG H 98 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.348A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA L 90 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN L 43 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS L 51 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.526A pdb=" N TYR L 31 " --> pdb=" O LYS L 36 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 1141 hydrogen bonds defined for protein. 3150 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: 7.52 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9059 1.34 - 1.47: 7519 1.47 - 1.59: 12587 1.59 - 1.72: 0 1.72 - 1.84: 156 Bond restraints: 29321 Sorted by residual: bond pdb=" N PRO C 817 " pdb=" CD PRO C 817 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N LEU A 303 " pdb=" CA LEU A 303 " ideal model delta sigma weight residual 1.456 1.503 -0.046 1.31e-02 5.83e+03 1.24e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.74e+00 ... (remaining 29316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 38695 1.79 - 3.58: 1083 3.58 - 5.37: 101 5.37 - 7.16: 27 7.16 - 8.96: 5 Bond angle restraints: 39911 Sorted by residual: angle pdb=" C SER B 659 " pdb=" CA SER B 659 " pdb=" CB SER B 659 " ideal model delta sigma weight residual 110.24 117.20 -6.96 1.46e+00 4.69e-01 2.27e+01 angle pdb=" N LEU L 53 " pdb=" CA LEU L 53 " pdb=" C LEU L 53 " ideal model delta sigma weight residual 110.42 103.85 6.57 1.55e+00 4.16e-01 1.79e+01 angle pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " pdb=" CG PHE B 377 " ideal model delta sigma weight residual 113.80 117.84 -4.04 1.00e+00 1.00e+00 1.63e+01 angle pdb=" N ILE B1018 " pdb=" CA ILE B1018 " pdb=" C ILE B1018 " ideal model delta sigma weight residual 110.62 114.60 -3.98 1.02e+00 9.61e-01 1.52e+01 angle pdb=" N GLN B 774 " pdb=" CA GLN B 774 " pdb=" C GLN B 774 " ideal model delta sigma weight residual 111.07 106.94 4.13 1.07e+00 8.73e-01 1.49e+01 ... (remaining 39906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16504 17.98 - 35.97: 1492 35.97 - 53.95: 394 53.95 - 71.93: 72 71.93 - 89.91: 30 Dihedral angle restraints: 18492 sinusoidal: 8253 harmonic: 10239 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -151.41 65.41 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -145.42 59.42 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 142.50 -49.50 1 1.00e+01 1.00e-02 3.36e+01 ... (remaining 18489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4532 0.106 - 0.212: 175 0.212 - 0.319: 12 0.319 - 0.425: 3 0.425 - 0.531: 1 Chirality restraints: 4723 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.65e+01 chirality pdb=" C1 NAG A1401 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG A1401 " pdb=" O5 NAG A1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.05e+00 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 -2.35 -0.05 2.00e-02 2.50e+03 5.19e+00 ... (remaining 4720 not shown) Planarity restraints: 5117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1201 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG C1201 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1201 " 0.106 2.00e-02 2.50e+03 pdb=" N2 NAG C1201 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG C1201 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " 0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG Y 2 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " 0.097 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1208 " -0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG B1208 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1208 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG B1208 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG B1208 " -0.161 2.00e-02 2.50e+03 ... (remaining 5114 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3669 2.75 - 3.29: 26190 3.29 - 3.83: 45602 3.83 - 4.36: 53438 4.36 - 4.90: 94833 Nonbonded interactions: 223732 Sorted by model distance: nonbonded pdb=" OH TYR A 248 " pdb=" O SER A 256 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 711 " pdb=" OE1 GLN B 895 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN B1135 " pdb=" N THR B1136 " model vdw 2.279 3.120 nonbonded pdb=" O TYR A 145 " pdb=" OH TYR H 102 " model vdw 2.286 3.040 nonbonded pdb=" OE2 GLU A 406 " pdb=" NZ LYS A 417 " model vdw 2.292 3.120 ... (remaining 223727 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 70 or resid 76 through 1407)) selection = (chain 'B' and (resid 14 through 175 or resid 185 through 1207)) selection = (chain 'C' and (resid 14 through 175 or resid 185 through 1207)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } 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=0.00 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: 2.460 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: 0.040 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.120 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29449 Z= 0.206 Angle : 0.721 17.029 40248 Z= 0.357 Chirality : 0.050 0.531 4723 Planarity : 0.013 0.300 5064 Dihedral : 14.732 89.913 11781 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.03 % Allowed : 13.07 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.62 (0.13), residues: 3488 helix: 1.23 (0.20), residues: 692 sheet: 0.90 (0.18), residues: 797 loop : -1.67 (0.12), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.028 0.001 TYR L 55 PHE 0.029 0.002 PHE C 377 TRP 0.025 0.002 TRP H 50 HIS 0.012 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00432 (29321) covalent geometry : angle 0.66185 (39911) SS BOND : bond 0.00349 ( 47) SS BOND : angle 1.57015 ( 94) hydrogen bonds : bond 0.17485 ( 1076) hydrogen bonds : angle 7.76701 ( 3150) link_BETA1-4 : bond 0.00748 ( 28) link_BETA1-4 : angle 2.00971 ( 84) link_NAG-ASN : bond 0.00767 ( 53) link_NAG-ASN : angle 4.25821 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 631 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8121 (m) cc_final: 0.7803 (p) REVERT: A 324 GLU cc_start: 0.8213 (pt0) cc_final: 0.8006 (pt0) REVERT: A 450 ASN cc_start: 0.7725 (m-40) cc_final: 0.7277 (m110) REVERT: A 695 TYR cc_start: 0.7883 (p90) cc_final: 0.7156 (p90) REVERT: A 949 GLN cc_start: 0.8454 (mm110) cc_final: 0.8001 (mm-40) REVERT: A 1072 GLU cc_start: 0.7459 (pm20) cc_final: 0.7241 (pm20) REVERT: B 28 TYR cc_start: 0.8219 (m-80) cc_final: 0.7907 (m-80) REVERT: B 202 LYS cc_start: 0.7641 (mttt) cc_final: 0.7421 (mttm) REVERT: B 271 GLN cc_start: 0.7735 (mt0) cc_final: 0.7490 (mt0) REVERT: B 373 SER cc_start: 0.8151 (p) cc_final: 0.7847 (t) REVERT: B 378 LYS cc_start: 0.7926 (mttt) cc_final: 0.7680 (ttmm) REVERT: B 571 ASP cc_start: 0.7505 (t0) cc_final: 0.7225 (t0) REVERT: B 714 ILE cc_start: 0.7961 (mm) cc_final: 0.7753 (mt) REVERT: B 772 VAL cc_start: 0.8458 (m) cc_final: 0.8248 (t) REVERT: B 882 ILE cc_start: 0.8447 (pt) cc_final: 0.8132 (mt) REVERT: B 979 ASP cc_start: 0.7506 (t70) cc_final: 0.7109 (t0) REVERT: C 191 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7829 (mt-10) REVERT: C 296 LEU cc_start: 0.7763 (tp) cc_final: 0.7465 (tt) REVERT: C 378 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7638 (mtpp) REVERT: C 440 ASN cc_start: 0.7716 (m110) cc_final: 0.7499 (m110) REVERT: C 529 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7882 (mmtt) REVERT: C 558 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7904 (mtmt) REVERT: C 571 ASP cc_start: 0.7921 (t70) cc_final: 0.6985 (t0) REVERT: C 736 VAL cc_start: 0.8435 (t) cc_final: 0.8208 (p) REVERT: C 772 VAL cc_start: 0.8675 (p) cc_final: 0.8416 (m) REVERT: C 1005 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7998 (tp40) REVERT: C 1072 GLU cc_start: 0.7857 (pm20) cc_final: 0.7564 (pm20) REVERT: C 1075 PHE cc_start: 0.7578 (m-80) cc_final: 0.7271 (m-80) outliers start: 1 outliers final: 0 residues processed: 632 average time/residue: 0.1831 time to fit residues: 180.7909 Evaluate side-chains 592 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 115 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 658 ASN B 501 ASN B 613 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115714 restraints weight = 41377.271| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.52 r_work: 0.3334 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29449 Z= 0.210 Angle : 0.695 13.635 40248 Z= 0.338 Chirality : 0.049 0.418 4723 Planarity : 0.005 0.057 5064 Dihedral : 8.154 59.965 5491 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.28 % Allowed : 13.11 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.55 (0.13), residues: 3488 helix: 1.36 (0.20), residues: 679 sheet: 0.84 (0.18), residues: 826 loop : -1.62 (0.12), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 567 TYR 0.019 0.002 TYR B1067 PHE 0.026 0.002 PHE C 970 TRP 0.018 0.002 TRP H 47 HIS 0.008 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00492 (29321) covalent geometry : angle 0.63866 (39911) SS BOND : bond 0.00576 ( 47) SS BOND : angle 2.32838 ( 94) hydrogen bonds : bond 0.05061 ( 1076) hydrogen bonds : angle 6.10997 ( 3150) link_BETA1-4 : bond 0.00647 ( 28) link_BETA1-4 : angle 1.68975 ( 84) link_NAG-ASN : bond 0.00772 ( 53) link_NAG-ASN : angle 3.89660 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 610 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8690 (mttp) cc_final: 0.8470 (mttp) REVERT: A 52 GLN cc_start: 0.8851 (tt0) cc_final: 0.8580 (tt0) REVERT: A 95 THR cc_start: 0.8213 (m) cc_final: 0.7778 (p) REVERT: A 191 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7893 (mt-10) REVERT: A 266 TYR cc_start: 0.8618 (m-80) cc_final: 0.8343 (m-80) REVERT: A 450 ASN cc_start: 0.7938 (m-40) cc_final: 0.7439 (m110) REVERT: A 516 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 695 TYR cc_start: 0.7977 (p90) cc_final: 0.7173 (p90) REVERT: A 739 THR cc_start: 0.8462 (m) cc_final: 0.8145 (p) REVERT: A 949 GLN cc_start: 0.8546 (mm110) cc_final: 0.8101 (mm-40) REVERT: B 153 MET cc_start: 0.6917 (mmm) cc_final: 0.6696 (mmm) REVERT: B 188 ASN cc_start: 0.7712 (m-40) cc_final: 0.7287 (m-40) REVERT: B 281 GLU cc_start: 0.7884 (pm20) cc_final: 0.7545 (pm20) REVERT: B 373 SER cc_start: 0.8217 (p) cc_final: 0.7937 (t) REVERT: B 377 PHE cc_start: 0.8558 (t80) cc_final: 0.8324 (t80) REVERT: B 378 LYS cc_start: 0.8296 (mttt) cc_final: 0.7946 (ttmm) REVERT: B 493 GLN cc_start: 0.7628 (tp40) cc_final: 0.7106 (tp40) REVERT: B 571 ASP cc_start: 0.7771 (t0) cc_final: 0.7356 (t0) REVERT: B 634 ARG cc_start: 0.8753 (mtp85) cc_final: 0.8491 (mtp-110) REVERT: B 747 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7527 (t) REVERT: B 979 ASP cc_start: 0.7760 (t70) cc_final: 0.7345 (t0) REVERT: C 96 GLU cc_start: 0.7275 (mt-10) cc_final: 0.7005 (mt-10) REVERT: C 200 TYR cc_start: 0.8006 (m-80) cc_final: 0.7752 (m-80) REVERT: C 227 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8107 (t) REVERT: C 304 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7993 (mptt) REVERT: C 430 THR cc_start: 0.7856 (m) cc_final: 0.7318 (p) REVERT: C 440 ASN cc_start: 0.7971 (m110) cc_final: 0.7733 (m110) REVERT: C 495 TYR cc_start: 0.7764 (m-80) cc_final: 0.6872 (m-80) REVERT: C 529 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7936 (mmtt) REVERT: C 558 LYS cc_start: 0.8314 (mtmt) cc_final: 0.8000 (mtmt) REVERT: C 571 ASP cc_start: 0.8039 (t70) cc_final: 0.7132 (t0) REVERT: C 772 VAL cc_start: 0.8682 (p) cc_final: 0.8441 (m) REVERT: C 1005 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8067 (tp40) REVERT: C 1072 GLU cc_start: 0.8083 (pm20) cc_final: 0.7712 (pm20) REVERT: C 1073 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7682 (mtpp) outliers start: 70 outliers final: 46 residues processed: 645 average time/residue: 0.1789 time to fit residues: 181.8482 Evaluate side-chains 606 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 557 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 134 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 320 optimal weight: 0.9980 chunk 327 optimal weight: 0.5980 chunk 104 optimal weight: 0.4980 chunk 109 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN B 66 HIS B 207 HIS B 501 ASN B 613 GLN B 804 GLN B 901 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116191 restraints weight = 41420.313| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.52 r_work: 0.3351 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29449 Z= 0.139 Angle : 0.649 16.171 40248 Z= 0.311 Chirality : 0.047 0.469 4723 Planarity : 0.004 0.054 5064 Dihedral : 7.442 59.997 5491 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.58 % Allowed : 14.41 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.48 (0.14), residues: 3488 helix: 1.37 (0.20), residues: 695 sheet: 0.83 (0.18), residues: 797 loop : -1.52 (0.12), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 454 TYR 0.017 0.001 TYR B1067 PHE 0.020 0.001 PHE B 541 TRP 0.016 0.001 TRP H 47 HIS 0.011 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00319 (29321) covalent geometry : angle 0.58928 (39911) SS BOND : bond 0.00609 ( 47) SS BOND : angle 2.31021 ( 94) hydrogen bonds : bond 0.04217 ( 1076) hydrogen bonds : angle 5.68329 ( 3150) link_BETA1-4 : bond 0.00578 ( 28) link_BETA1-4 : angle 1.58977 ( 84) link_NAG-ASN : bond 0.00842 ( 53) link_NAG-ASN : angle 3.85721 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 584 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8233 (m) cc_final: 0.7805 (p) REVERT: A 306 PHE cc_start: 0.9015 (m-80) cc_final: 0.8746 (m-10) REVERT: A 414 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7873 (mm-40) REVERT: A 450 ASN cc_start: 0.7973 (m-40) cc_final: 0.7519 (m110) REVERT: A 516 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 643 PHE cc_start: 0.8287 (t80) cc_final: 0.8032 (t80) REVERT: A 660 TYR cc_start: 0.8448 (m-10) cc_final: 0.8197 (m-10) REVERT: A 695 TYR cc_start: 0.8117 (p90) cc_final: 0.7336 (p90) REVERT: A 949 GLN cc_start: 0.8552 (mm110) cc_final: 0.8061 (mm-40) REVERT: A 979 ASP cc_start: 0.8050 (t0) cc_final: 0.7742 (t0) REVERT: A 1130 ILE cc_start: 0.8099 (pt) cc_final: 0.7531 (mt) REVERT: B 153 MET cc_start: 0.6983 (mmm) cc_final: 0.6774 (mmm) REVERT: B 188 ASN cc_start: 0.7728 (m-40) cc_final: 0.7264 (m-40) REVERT: B 281 GLU cc_start: 0.7855 (pm20) cc_final: 0.7549 (pm20) REVERT: B 373 SER cc_start: 0.8208 (p) cc_final: 0.7961 (t) REVERT: B 376 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7947 (p) REVERT: B 378 LYS cc_start: 0.8393 (mttt) cc_final: 0.8072 (ttmm) REVERT: B 571 ASP cc_start: 0.7815 (t0) cc_final: 0.7369 (t0) REVERT: B 654 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8024 (mt-10) REVERT: B 773 GLU cc_start: 0.7887 (tt0) cc_final: 0.7534 (tt0) REVERT: B 775 ASP cc_start: 0.8065 (m-30) cc_final: 0.7801 (m-30) REVERT: B 979 ASP cc_start: 0.7768 (t70) cc_final: 0.7323 (t0) REVERT: C 96 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6868 (mt-10) REVERT: C 158 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7776 (mtt90) REVERT: C 200 TYR cc_start: 0.8023 (m-80) cc_final: 0.7637 (m-80) REVERT: C 304 LYS cc_start: 0.8205 (mmtp) cc_final: 0.7967 (mptt) REVERT: C 338 PHE cc_start: 0.8323 (m-80) cc_final: 0.7847 (m-80) REVERT: C 374 PHE cc_start: 0.8456 (m-80) cc_final: 0.8238 (m-80) REVERT: C 430 THR cc_start: 0.7814 (m) cc_final: 0.7464 (p) REVERT: C 440 ASN cc_start: 0.8005 (m110) cc_final: 0.7762 (m110) REVERT: C 529 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7896 (mmtt) REVERT: C 558 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7978 (mtmt) REVERT: C 571 ASP cc_start: 0.8003 (t70) cc_final: 0.7191 (t0) REVERT: C 772 VAL cc_start: 0.8671 (p) cc_final: 0.8424 (m) REVERT: C 801 ASN cc_start: 0.7814 (m-40) cc_final: 0.7611 (m-40) REVERT: C 1055 SER cc_start: 0.8775 (m) cc_final: 0.8545 (t) REVERT: C 1072 GLU cc_start: 0.8104 (pm20) cc_final: 0.7751 (pm20) REVERT: C 1141 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7891 (tt) outliers start: 79 outliers final: 47 residues processed: 620 average time/residue: 0.1789 time to fit residues: 175.0542 Evaluate side-chains 618 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 569 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 100 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 277 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 279 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 360 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** L 95 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 = 0.3812 r_free = 0.3812 target = 0.141240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114930 restraints weight = 41328.912| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.50 r_work: 0.3337 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29449 Z= 0.171 Angle : 0.649 17.389 40248 Z= 0.313 Chirality : 0.047 0.408 4723 Planarity : 0.004 0.055 5064 Dihedral : 6.968 57.711 5491 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.00 % Allowed : 14.84 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.49 (0.14), residues: 3488 helix: 1.39 (0.20), residues: 688 sheet: 0.78 (0.18), residues: 766 loop : -1.47 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.018 0.001 TYR B1067 PHE 0.021 0.002 PHE B 541 TRP 0.014 0.001 TRP H 47 HIS 0.013 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00404 (29321) covalent geometry : angle 0.59293 (39911) SS BOND : bond 0.00645 ( 47) SS BOND : angle 2.41846 ( 94) hydrogen bonds : bond 0.04321 ( 1076) hydrogen bonds : angle 5.53606 ( 3150) link_BETA1-4 : bond 0.00531 ( 28) link_BETA1-4 : angle 1.44791 ( 84) link_NAG-ASN : bond 0.00755 ( 53) link_NAG-ASN : angle 3.72206 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 589 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7561 (m-40) cc_final: 0.7348 (m-40) REVERT: A 95 THR cc_start: 0.8238 (m) cc_final: 0.7784 (p) REVERT: A 138 ASP cc_start: 0.7251 (t0) cc_final: 0.6951 (p0) REVERT: A 266 TYR cc_start: 0.8596 (m-80) cc_final: 0.8367 (m-80) REVERT: A 306 PHE cc_start: 0.9041 (m-80) cc_final: 0.8732 (m-10) REVERT: A 450 ASN cc_start: 0.7986 (m-40) cc_final: 0.7527 (m110) REVERT: A 516 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7319 (mm-30) REVERT: A 643 PHE cc_start: 0.8277 (t80) cc_final: 0.8005 (t80) REVERT: A 660 TYR cc_start: 0.8445 (m-10) cc_final: 0.8202 (m-10) REVERT: A 695 TYR cc_start: 0.8185 (p90) cc_final: 0.7383 (p90) REVERT: A 803 SER cc_start: 0.8379 (t) cc_final: 0.8060 (p) REVERT: A 825 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8440 (mttm) REVERT: A 949 GLN cc_start: 0.8562 (mm110) cc_final: 0.8357 (mm110) REVERT: A 979 ASP cc_start: 0.8062 (t0) cc_final: 0.7652 (t0) REVERT: B 66 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5762 (p90) REVERT: B 78 ARG cc_start: 0.7368 (ttm170) cc_final: 0.5908 (ttp-110) REVERT: B 188 ASN cc_start: 0.7795 (m-40) cc_final: 0.7207 (m-40) REVERT: B 207 HIS cc_start: 0.7837 (t70) cc_final: 0.7339 (t-170) REVERT: B 281 GLU cc_start: 0.7887 (pm20) cc_final: 0.7529 (pm20) REVERT: B 373 SER cc_start: 0.8219 (p) cc_final: 0.8000 (t) REVERT: B 376 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7947 (p) REVERT: B 378 LYS cc_start: 0.8431 (mttt) cc_final: 0.8096 (ttmm) REVERT: B 398 ASP cc_start: 0.7998 (m-30) cc_final: 0.7756 (m-30) REVERT: B 571 ASP cc_start: 0.7830 (t0) cc_final: 0.7342 (t0) REVERT: B 654 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8047 (mt-10) REVERT: B 819 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7575 (mt-10) REVERT: B 979 ASP cc_start: 0.7753 (t70) cc_final: 0.7324 (t0) REVERT: C 53 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7794 (t0) REVERT: C 158 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7775 (mtt90) REVERT: C 200 TYR cc_start: 0.8039 (m-80) cc_final: 0.7598 (m-80) REVERT: C 304 LYS cc_start: 0.8209 (mmtp) cc_final: 0.7968 (mptt) REVERT: C 374 PHE cc_start: 0.8458 (m-80) cc_final: 0.8141 (m-80) REVERT: C 430 THR cc_start: 0.7851 (m) cc_final: 0.7496 (p) REVERT: C 440 ASN cc_start: 0.8022 (m110) cc_final: 0.7785 (m110) REVERT: C 516 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7721 (mt-10) REVERT: C 529 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7923 (mmtt) REVERT: C 558 LYS cc_start: 0.8342 (mtmt) cc_final: 0.8009 (mtmt) REVERT: C 571 ASP cc_start: 0.8108 (t70) cc_final: 0.7251 (t0) REVERT: C 772 VAL cc_start: 0.8659 (p) cc_final: 0.8419 (m) REVERT: C 801 ASN cc_start: 0.7879 (m-40) cc_final: 0.7662 (m-40) REVERT: C 804 GLN cc_start: 0.8232 (mt0) cc_final: 0.7910 (mp10) REVERT: C 949 GLN cc_start: 0.8594 (tp40) cc_final: 0.8365 (tp-100) REVERT: C 1072 GLU cc_start: 0.8104 (pm20) cc_final: 0.7746 (pm20) REVERT: C 1141 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7792 (tt) outliers start: 92 outliers final: 61 residues processed: 637 average time/residue: 0.1786 time to fit residues: 179.6118 Evaluate side-chains 634 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 569 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 658 ASN A1106 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 501 ASN B 613 GLN B 804 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114917 restraints weight = 41558.001| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.51 r_work: 0.3333 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 29449 Z= 0.177 Angle : 0.659 14.822 40248 Z= 0.318 Chirality : 0.048 0.520 4723 Planarity : 0.004 0.054 5064 Dihedral : 6.668 57.849 5491 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.06 % Allowed : 15.39 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.51 (0.13), residues: 3488 helix: 1.41 (0.20), residues: 681 sheet: 0.68 (0.18), residues: 771 loop : -1.45 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.017 0.001 TYR C1067 PHE 0.021 0.002 PHE B 541 TRP 0.012 0.001 TRP H 47 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00420 (29321) covalent geometry : angle 0.60248 (39911) SS BOND : bond 0.00868 ( 47) SS BOND : angle 2.52889 ( 94) hydrogen bonds : bond 0.04353 ( 1076) hydrogen bonds : angle 5.46643 ( 3150) link_BETA1-4 : bond 0.00570 ( 28) link_BETA1-4 : angle 1.61719 ( 84) link_NAG-ASN : bond 0.00631 ( 53) link_NAG-ASN : angle 3.70957 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 593 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7784 (p0) cc_final: 0.7549 (p0) REVERT: A 95 THR cc_start: 0.8212 (m) cc_final: 0.7742 (p) REVERT: A 280 ASN cc_start: 0.7933 (t0) cc_final: 0.7680 (t0) REVERT: A 281 GLU cc_start: 0.8152 (pt0) cc_final: 0.7923 (pt0) REVERT: A 306 PHE cc_start: 0.9068 (m-80) cc_final: 0.8778 (m-10) REVERT: A 414 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7972 (mm-40) REVERT: A 438 SER cc_start: 0.8402 (t) cc_final: 0.8029 (t) REVERT: A 450 ASN cc_start: 0.8013 (m-40) cc_final: 0.7544 (m110) REVERT: A 516 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 556 ASN cc_start: 0.7699 (p0) cc_final: 0.7379 (p0) REVERT: A 803 SER cc_start: 0.8397 (t) cc_final: 0.8050 (p) REVERT: A 825 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8456 (mttm) REVERT: A 949 GLN cc_start: 0.8556 (mm110) cc_final: 0.8350 (mm110) REVERT: A 979 ASP cc_start: 0.8040 (t0) cc_final: 0.7594 (t0) REVERT: A 1132 ILE cc_start: 0.8306 (tt) cc_final: 0.8067 (tp) REVERT: B 66 HIS cc_start: 0.6296 (OUTLIER) cc_final: 0.5791 (p90) REVERT: B 78 ARG cc_start: 0.7335 (ttm170) cc_final: 0.6162 (ttm-80) REVERT: B 188 ASN cc_start: 0.7770 (m-40) cc_final: 0.7141 (m-40) REVERT: B 207 HIS cc_start: 0.7762 (t-90) cc_final: 0.7235 (t-170) REVERT: B 281 GLU cc_start: 0.7866 (pm20) cc_final: 0.7496 (pm20) REVERT: B 373 SER cc_start: 0.8196 (p) cc_final: 0.7960 (t) REVERT: B 376 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7938 (p) REVERT: B 378 LYS cc_start: 0.8447 (mttt) cc_final: 0.8092 (ttmm) REVERT: B 398 ASP cc_start: 0.8034 (m-30) cc_final: 0.7779 (m-30) REVERT: B 571 ASP cc_start: 0.7822 (t0) cc_final: 0.7335 (t0) REVERT: B 819 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7558 (mt-10) REVERT: B 882 ILE cc_start: 0.8377 (pt) cc_final: 0.8088 (mt) REVERT: B 905 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7217 (mtt180) REVERT: B 979 ASP cc_start: 0.7737 (t70) cc_final: 0.7328 (t0) REVERT: C 132 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7391 (mt-10) REVERT: C 158 ARG cc_start: 0.8039 (mtt90) cc_final: 0.7504 (mtt90) REVERT: C 200 TYR cc_start: 0.8034 (m-80) cc_final: 0.7580 (m-80) REVERT: C 516 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7765 (mt-10) REVERT: C 529 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7916 (mmtt) REVERT: C 558 LYS cc_start: 0.8349 (mtmt) cc_final: 0.7971 (mtmt) REVERT: C 571 ASP cc_start: 0.8084 (t70) cc_final: 0.7857 (t0) REVERT: C 772 VAL cc_start: 0.8618 (p) cc_final: 0.8382 (m) REVERT: C 787 GLN cc_start: 0.8505 (mt0) cc_final: 0.8090 (mt0) REVERT: C 801 ASN cc_start: 0.7834 (m-40) cc_final: 0.7586 (m-40) REVERT: C 804 GLN cc_start: 0.8250 (mt0) cc_final: 0.7950 (mp10) REVERT: C 949 GLN cc_start: 0.8552 (tp40) cc_final: 0.8330 (tp-100) REVERT: C 1072 GLU cc_start: 0.8123 (pm20) cc_final: 0.7712 (pm20) REVERT: C 1141 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7658 (tt) outliers start: 94 outliers final: 75 residues processed: 645 average time/residue: 0.1753 time to fit residues: 177.3584 Evaluate side-chains 655 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 577 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 152 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 245 HIS A 658 ASN A 935 GLN A1083 HIS B 30 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 935 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115374 restraints weight = 41313.281| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.48 r_work: 0.3339 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29449 Z= 0.157 Angle : 0.673 17.167 40248 Z= 0.318 Chirality : 0.053 1.234 4723 Planarity : 0.004 0.054 5064 Dihedral : 6.557 58.056 5491 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 3.10 % Allowed : 16.11 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3488 helix: 1.49 (0.20), residues: 680 sheet: 0.70 (0.18), residues: 769 loop : -1.39 (0.12), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.018 0.001 TYR C 707 PHE 0.023 0.001 PHE B 541 TRP 0.012 0.001 TRP H 47 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00369 (29321) covalent geometry : angle 0.60924 (39911) SS BOND : bond 0.00641 ( 47) SS BOND : angle 2.36658 ( 94) hydrogen bonds : bond 0.04188 ( 1076) hydrogen bonds : angle 5.35620 ( 3150) link_BETA1-4 : bond 0.00523 ( 28) link_BETA1-4 : angle 1.55638 ( 84) link_NAG-ASN : bond 0.00718 ( 53) link_NAG-ASN : angle 4.10366 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 598 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7812 (p0) cc_final: 0.7478 (p0) REVERT: A 95 THR cc_start: 0.8127 (m) cc_final: 0.7687 (p) REVERT: A 280 ASN cc_start: 0.7906 (t0) cc_final: 0.7660 (t0) REVERT: A 281 GLU cc_start: 0.8160 (pt0) cc_final: 0.7906 (pt0) REVERT: A 306 PHE cc_start: 0.9041 (m-80) cc_final: 0.8756 (m-10) REVERT: A 414 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7961 (mm-40) REVERT: A 438 SER cc_start: 0.8379 (t) cc_final: 0.7988 (t) REVERT: A 450 ASN cc_start: 0.7989 (m-40) cc_final: 0.7535 (m110) REVERT: A 516 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7264 (mm-30) REVERT: A 556 ASN cc_start: 0.7722 (p0) cc_final: 0.7374 (p0) REVERT: A 803 SER cc_start: 0.8391 (t) cc_final: 0.8033 (p) REVERT: A 825 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8518 (mttm) REVERT: A 979 ASP cc_start: 0.8042 (t0) cc_final: 0.7614 (t0) REVERT: A 1132 ILE cc_start: 0.8290 (tt) cc_final: 0.8061 (tp) REVERT: B 66 HIS cc_start: 0.6359 (OUTLIER) cc_final: 0.5925 (p90) REVERT: B 78 ARG cc_start: 0.7351 (ttm170) cc_final: 0.6209 (ttm-80) REVERT: B 188 ASN cc_start: 0.7728 (m-40) cc_final: 0.7200 (m-40) REVERT: B 207 HIS cc_start: 0.7788 (t-90) cc_final: 0.7346 (t-170) REVERT: B 281 GLU cc_start: 0.7855 (pm20) cc_final: 0.7466 (pm20) REVERT: B 373 SER cc_start: 0.8137 (p) cc_final: 0.7922 (t) REVERT: B 378 LYS cc_start: 0.8397 (mttt) cc_final: 0.8057 (ttmm) REVERT: B 398 ASP cc_start: 0.8023 (m-30) cc_final: 0.7776 (m-30) REVERT: B 484 GLU cc_start: 0.7822 (tt0) cc_final: 0.7574 (tt0) REVERT: B 571 ASP cc_start: 0.7818 (t0) cc_final: 0.7306 (t0) REVERT: B 643 PHE cc_start: 0.8343 (t80) cc_final: 0.7721 (t80) REVERT: B 654 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7981 (mt-10) REVERT: B 655 HIS cc_start: 0.8446 (t70) cc_final: 0.8193 (t70) REVERT: B 773 GLU cc_start: 0.8052 (tp30) cc_final: 0.7666 (tt0) REVERT: B 780 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7272 (mt-10) REVERT: B 882 ILE cc_start: 0.8348 (pt) cc_final: 0.8073 (mt) REVERT: B 905 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7140 (mtt180) REVERT: B 955 ASN cc_start: 0.7809 (m-40) cc_final: 0.7517 (t0) REVERT: B 979 ASP cc_start: 0.7693 (t70) cc_final: 0.7329 (t0) REVERT: B 1038 LYS cc_start: 0.8630 (mttp) cc_final: 0.8419 (mptp) REVERT: B 1050 MET cc_start: 0.8273 (ptt) cc_final: 0.7965 (ptp) REVERT: B 1072 GLU cc_start: 0.8496 (pm20) cc_final: 0.7897 (mp0) REVERT: C 132 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7336 (mt-10) REVERT: C 158 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7564 (mtt90) REVERT: C 200 TYR cc_start: 0.8025 (m-80) cc_final: 0.7560 (m-80) REVERT: C 374 PHE cc_start: 0.8419 (m-80) cc_final: 0.8212 (m-80) REVERT: C 516 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7737 (mt-10) REVERT: C 529 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7905 (mmtt) REVERT: C 571 ASP cc_start: 0.8062 (t70) cc_final: 0.7833 (t0) REVERT: C 772 VAL cc_start: 0.8599 (p) cc_final: 0.8364 (m) REVERT: C 787 GLN cc_start: 0.8521 (mt0) cc_final: 0.8101 (mt0) REVERT: C 801 ASN cc_start: 0.7815 (m-40) cc_final: 0.7554 (m-40) REVERT: C 804 GLN cc_start: 0.8245 (mt0) cc_final: 0.7943 (mp10) REVERT: C 949 GLN cc_start: 0.8545 (tp40) cc_final: 0.8318 (tp-100) REVERT: C 1072 GLU cc_start: 0.8103 (pm20) cc_final: 0.7850 (pm20) REVERT: C 1141 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7672 (tt) outliers start: 95 outliers final: 68 residues processed: 654 average time/residue: 0.1780 time to fit residues: 183.2789 Evaluate side-chains 660 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 590 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 346 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 347 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 329 optimal weight: 0.7980 chunk 302 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 658 ASN A1101 HIS B 30 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 501 ASN B 804 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115514 restraints weight = 41362.092| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.51 r_work: 0.3337 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29449 Z= 0.149 Angle : 0.665 14.706 40248 Z= 0.317 Chirality : 0.051 0.967 4723 Planarity : 0.004 0.053 5064 Dihedral : 6.435 57.950 5491 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.06 % Allowed : 16.76 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.41 (0.14), residues: 3488 helix: 1.51 (0.20), residues: 686 sheet: 0.65 (0.18), residues: 773 loop : -1.35 (0.12), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.017 0.001 TYR B1067 PHE 0.023 0.001 PHE B 541 TRP 0.013 0.001 TRP A 64 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00349 (29321) covalent geometry : angle 0.60527 (39911) SS BOND : bond 0.00666 ( 47) SS BOND : angle 2.40750 ( 94) hydrogen bonds : bond 0.04098 ( 1076) hydrogen bonds : angle 5.27617 ( 3150) link_BETA1-4 : bond 0.00516 ( 28) link_BETA1-4 : angle 1.50816 ( 84) link_NAG-ASN : bond 0.00749 ( 53) link_NAG-ASN : angle 3.89817 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 595 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7788 (p0) cc_final: 0.7558 (p0) REVERT: A 95 THR cc_start: 0.8123 (m) cc_final: 0.7679 (p) REVERT: A 280 ASN cc_start: 0.7858 (t0) cc_final: 0.7610 (t0) REVERT: A 281 GLU cc_start: 0.8189 (pt0) cc_final: 0.7933 (pt0) REVERT: A 306 PHE cc_start: 0.9038 (m-80) cc_final: 0.8768 (m-10) REVERT: A 414 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8010 (mm-40) REVERT: A 438 SER cc_start: 0.8380 (t) cc_final: 0.7986 (t) REVERT: A 450 ASN cc_start: 0.7996 (m-40) cc_final: 0.7551 (m110) REVERT: A 556 ASN cc_start: 0.7753 (p0) cc_final: 0.7378 (p0) REVERT: A 803 SER cc_start: 0.8400 (t) cc_final: 0.8046 (p) REVERT: A 825 LYS cc_start: 0.8842 (ttmm) cc_final: 0.8596 (mtpt) REVERT: A 979 ASP cc_start: 0.8035 (t0) cc_final: 0.7579 (t0) REVERT: A 1132 ILE cc_start: 0.8303 (tt) cc_final: 0.8077 (tp) REVERT: B 66 HIS cc_start: 0.6418 (OUTLIER) cc_final: 0.5822 (p90) REVERT: B 78 ARG cc_start: 0.7407 (ttm170) cc_final: 0.6456 (ttm-80) REVERT: B 188 ASN cc_start: 0.7712 (m-40) cc_final: 0.7162 (m-40) REVERT: B 207 HIS cc_start: 0.7908 (t-90) cc_final: 0.7384 (t-170) REVERT: B 281 GLU cc_start: 0.7842 (pm20) cc_final: 0.7451 (pm20) REVERT: B 324 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 376 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7976 (p) REVERT: B 378 LYS cc_start: 0.8440 (mttt) cc_final: 0.8111 (ttmm) REVERT: B 398 ASP cc_start: 0.8021 (m-30) cc_final: 0.7770 (m-30) REVERT: B 467 ASP cc_start: 0.7950 (t0) cc_final: 0.7731 (t0) REVERT: B 484 GLU cc_start: 0.7866 (tt0) cc_final: 0.7621 (tt0) REVERT: B 571 ASP cc_start: 0.7815 (t0) cc_final: 0.7276 (t0) REVERT: B 643 PHE cc_start: 0.8367 (t80) cc_final: 0.7680 (t80) REVERT: B 655 HIS cc_start: 0.8456 (t70) cc_final: 0.8176 (t70) REVERT: B 804 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7979 (mp10) REVERT: B 882 ILE cc_start: 0.8323 (pt) cc_final: 0.8085 (mt) REVERT: B 905 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7220 (mtt180) REVERT: B 955 ASN cc_start: 0.7809 (m-40) cc_final: 0.7524 (t0) REVERT: B 979 ASP cc_start: 0.7740 (t70) cc_final: 0.7361 (t0) REVERT: B 1072 GLU cc_start: 0.8497 (pm20) cc_final: 0.7978 (mp0) REVERT: C 81 ASN cc_start: 0.8389 (p0) cc_final: 0.8184 (p0) REVERT: C 84 LEU cc_start: 0.8093 (mt) cc_final: 0.7850 (mp) REVERT: C 158 ARG cc_start: 0.8105 (mtt90) cc_final: 0.7568 (mtt90) REVERT: C 200 TYR cc_start: 0.7994 (m-80) cc_final: 0.7513 (m-80) REVERT: C 374 PHE cc_start: 0.8426 (m-80) cc_final: 0.8223 (m-80) REVERT: C 377 PHE cc_start: 0.8126 (t80) cc_final: 0.7889 (t80) REVERT: C 516 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7774 (mt-10) REVERT: C 529 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7939 (mmtt) REVERT: C 571 ASP cc_start: 0.8017 (t70) cc_final: 0.7791 (t0) REVERT: C 660 TYR cc_start: 0.8308 (m-10) cc_final: 0.7554 (m-80) REVERT: C 772 VAL cc_start: 0.8626 (p) cc_final: 0.8372 (m) REVERT: C 787 GLN cc_start: 0.8510 (mt0) cc_final: 0.8091 (mt0) REVERT: C 801 ASN cc_start: 0.7838 (m-40) cc_final: 0.7572 (m-40) REVERT: C 804 GLN cc_start: 0.8223 (mt0) cc_final: 0.7949 (mp10) REVERT: C 949 GLN cc_start: 0.8552 (tp40) cc_final: 0.8328 (tp-100) REVERT: C 1072 GLU cc_start: 0.8127 (pm20) cc_final: 0.7852 (pm20) REVERT: C 1141 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7701 (tt) outliers start: 94 outliers final: 70 residues processed: 646 average time/residue: 0.1757 time to fit residues: 180.0061 Evaluate side-chains 656 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 583 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 186 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 345 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 658 ASN B 30 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN B 957 GLN C 422 ASN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113062 restraints weight = 41516.161| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.49 r_work: 0.3302 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 29449 Z= 0.293 Angle : 0.752 15.483 40248 Z= 0.367 Chirality : 0.055 1.014 4723 Planarity : 0.005 0.058 5064 Dihedral : 6.569 58.822 5491 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.20 % Allowed : 17.12 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 3488 helix: 1.01 (0.20), residues: 698 sheet: 0.51 (0.18), residues: 793 loop : -1.46 (0.12), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.025 0.002 TYR B 204 PHE 0.028 0.002 PHE A1089 TRP 0.020 0.002 TRP A 64 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00700 (29321) covalent geometry : angle 0.69590 (39911) SS BOND : bond 0.00860 ( 47) SS BOND : angle 2.82653 ( 94) hydrogen bonds : bond 0.05231 ( 1076) hydrogen bonds : angle 5.54728 ( 3150) link_BETA1-4 : bond 0.00485 ( 28) link_BETA1-4 : angle 1.53057 ( 84) link_NAG-ASN : bond 0.00774 ( 53) link_NAG-ASN : angle 3.96094 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 600 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7918 (p0) cc_final: 0.7652 (p0) REVERT: A 95 THR cc_start: 0.8157 (m) cc_final: 0.7695 (p) REVERT: A 269 TYR cc_start: 0.8243 (m-80) cc_final: 0.7985 (m-80) REVERT: A 280 ASN cc_start: 0.7884 (t0) cc_final: 0.7638 (t0) REVERT: A 281 GLU cc_start: 0.8134 (pt0) cc_final: 0.7897 (pt0) REVERT: A 306 PHE cc_start: 0.9048 (m-80) cc_final: 0.8840 (m-10) REVERT: A 414 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7997 (mm-40) REVERT: A 420 ASP cc_start: 0.7695 (m-30) cc_final: 0.7278 (t0) REVERT: A 450 ASN cc_start: 0.8022 (m-40) cc_final: 0.7572 (m110) REVERT: A 484 GLU cc_start: 0.8496 (pt0) cc_final: 0.8295 (pt0) REVERT: A 739 THR cc_start: 0.8454 (m) cc_final: 0.8146 (p) REVERT: A 803 SER cc_start: 0.8489 (t) cc_final: 0.8088 (p) REVERT: A 804 GLN cc_start: 0.8572 (mm-40) cc_final: 0.7945 (mm-40) REVERT: A 825 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8596 (mtpt) REVERT: A 979 ASP cc_start: 0.8029 (t0) cc_final: 0.7559 (t0) REVERT: A 1132 ILE cc_start: 0.8374 (tt) cc_final: 0.8141 (tp) REVERT: B 66 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5796 (p90) REVERT: B 188 ASN cc_start: 0.7865 (m-40) cc_final: 0.7277 (m-40) REVERT: B 207 HIS cc_start: 0.7953 (t-90) cc_final: 0.7380 (t-170) REVERT: B 281 GLU cc_start: 0.7888 (pm20) cc_final: 0.7522 (pm20) REVERT: B 376 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8072 (p) REVERT: B 378 LYS cc_start: 0.8423 (mttt) cc_final: 0.8090 (ttmm) REVERT: B 406 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: B 467 ASP cc_start: 0.7944 (t0) cc_final: 0.7741 (t0) REVERT: B 484 GLU cc_start: 0.7836 (tt0) cc_final: 0.7590 (tt0) REVERT: B 571 ASP cc_start: 0.7845 (t0) cc_final: 0.7237 (t0) REVERT: B 882 ILE cc_start: 0.8340 (pt) cc_final: 0.8071 (mt) REVERT: B 955 ASN cc_start: 0.7887 (m-40) cc_final: 0.7582 (t0) REVERT: B 979 ASP cc_start: 0.7701 (t0) cc_final: 0.7336 (t0) REVERT: B 1038 LYS cc_start: 0.8658 (mttp) cc_final: 0.8444 (mptp) REVERT: B 1072 GLU cc_start: 0.8455 (pm20) cc_final: 0.7963 (mp0) REVERT: C 158 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7599 (mtt90) REVERT: C 200 TYR cc_start: 0.8097 (m-80) cc_final: 0.7712 (m-80) REVERT: C 516 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7675 (mt-10) REVERT: C 772 VAL cc_start: 0.8658 (p) cc_final: 0.8424 (m) REVERT: C 796 ASP cc_start: 0.7338 (t0) cc_final: 0.6931 (t70) REVERT: C 801 ASN cc_start: 0.8036 (m-40) cc_final: 0.7799 (m-40) REVERT: C 804 GLN cc_start: 0.8327 (mt0) cc_final: 0.8034 (mp10) REVERT: C 1072 GLU cc_start: 0.8117 (pm20) cc_final: 0.7908 (pm20) REVERT: C 1141 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7689 (tt) REVERT: C 1142 GLN cc_start: 0.7957 (tp40) cc_final: 0.7525 (tp40) outliers start: 98 outliers final: 80 residues processed: 649 average time/residue: 0.1748 time to fit residues: 179.1086 Evaluate side-chains 669 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 585 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 279 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 185 optimal weight: 0.7980 chunk 75 optimal weight: 0.0870 chunk 314 optimal weight: 0.8980 chunk 288 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 chunk 98 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 314 GLN A 360 ASN A 658 ASN B 30 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 762 GLN B 804 GLN B 955 ASN B1011 GLN C 935 GLN C 949 GLN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115903 restraints weight = 41224.157| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.51 r_work: 0.3330 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29449 Z= 0.129 Angle : 0.660 15.119 40248 Z= 0.316 Chirality : 0.050 0.887 4723 Planarity : 0.004 0.052 5064 Dihedral : 6.320 58.334 5491 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.41 % Allowed : 18.06 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3488 helix: 1.23 (0.20), residues: 715 sheet: 0.48 (0.18), residues: 794 loop : -1.37 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.018 0.001 TYR A 265 PHE 0.047 0.001 PHE A 140 TRP 0.014 0.001 TRP A 64 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00299 (29321) covalent geometry : angle 0.60471 (39911) SS BOND : bond 0.00620 ( 47) SS BOND : angle 2.25761 ( 94) hydrogen bonds : bond 0.04033 ( 1076) hydrogen bonds : angle 5.24804 ( 3150) link_BETA1-4 : bond 0.00487 ( 28) link_BETA1-4 : angle 1.52054 ( 84) link_NAG-ASN : bond 0.00790 ( 53) link_NAG-ASN : angle 3.79422 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 589 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7833 (p0) cc_final: 0.7566 (p0) REVERT: A 95 THR cc_start: 0.8028 (m) cc_final: 0.7561 (p) REVERT: A 138 ASP cc_start: 0.7728 (m-30) cc_final: 0.7362 (m-30) REVERT: A 269 TYR cc_start: 0.8178 (m-80) cc_final: 0.7913 (m-80) REVERT: A 280 ASN cc_start: 0.7838 (t0) cc_final: 0.7594 (t0) REVERT: A 281 GLU cc_start: 0.8149 (pt0) cc_final: 0.7858 (pt0) REVERT: A 306 PHE cc_start: 0.9015 (m-80) cc_final: 0.8787 (m-10) REVERT: A 357 ARG cc_start: 0.8042 (ttt90) cc_final: 0.7809 (ttt90) REVERT: A 414 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8022 (mm-40) REVERT: A 420 ASP cc_start: 0.7661 (m-30) cc_final: 0.7247 (t0) REVERT: A 438 SER cc_start: 0.8308 (t) cc_final: 0.7963 (t) REVERT: A 450 ASN cc_start: 0.7980 (m-40) cc_final: 0.7525 (m110) REVERT: A 803 SER cc_start: 0.8390 (t) cc_final: 0.8024 (p) REVERT: A 825 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8586 (mtpt) REVERT: A 979 ASP cc_start: 0.8028 (t0) cc_final: 0.7616 (t0) REVERT: B 66 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.5986 (p90) REVERT: B 188 ASN cc_start: 0.7680 (m-40) cc_final: 0.7299 (m-40) REVERT: B 207 HIS cc_start: 0.7887 (t-90) cc_final: 0.7612 (t-90) REVERT: B 281 GLU cc_start: 0.7868 (pm20) cc_final: 0.7451 (pm20) REVERT: B 378 LYS cc_start: 0.8401 (mttt) cc_final: 0.8068 (ttmm) REVERT: B 398 ASP cc_start: 0.8021 (m-30) cc_final: 0.7762 (m-30) REVERT: B 484 GLU cc_start: 0.7849 (tt0) cc_final: 0.7596 (tt0) REVERT: B 571 ASP cc_start: 0.7867 (t0) cc_final: 0.7277 (t0) REVERT: B 654 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 703 ASN cc_start: 0.8231 (t0) cc_final: 0.7536 (m-40) REVERT: B 775 ASP cc_start: 0.8032 (m-30) cc_final: 0.7817 (m-30) REVERT: B 804 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7961 (mp10) REVERT: B 882 ILE cc_start: 0.8310 (pt) cc_final: 0.8070 (mt) REVERT: B 905 ARG cc_start: 0.7541 (mtt180) cc_final: 0.7255 (mtt180) REVERT: B 933 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8214 (mtpp) REVERT: B 979 ASP cc_start: 0.7675 (t0) cc_final: 0.7272 (t0) REVERT: B 1072 GLU cc_start: 0.8494 (pm20) cc_final: 0.8014 (mp0) REVERT: C 131 CYS cc_start: 0.6603 (m) cc_final: 0.6322 (m) REVERT: C 158 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7364 (mtt90) REVERT: C 200 TYR cc_start: 0.8019 (m-80) cc_final: 0.7570 (m-80) REVERT: C 214 ARG cc_start: 0.7467 (ptm160) cc_final: 0.7228 (ptp90) REVERT: C 358 ILE cc_start: 0.8310 (mt) cc_final: 0.8107 (mm) REVERT: C 516 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 571 ASP cc_start: 0.7925 (t0) cc_final: 0.7624 (t0) REVERT: C 772 VAL cc_start: 0.8597 (p) cc_final: 0.8333 (m) REVERT: C 801 ASN cc_start: 0.7917 (m-40) cc_final: 0.7621 (m-40) REVERT: C 804 GLN cc_start: 0.8206 (mt0) cc_final: 0.7919 (mp10) REVERT: C 1072 GLU cc_start: 0.8101 (pm20) cc_final: 0.7833 (pm20) REVERT: C 1141 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7549 (tt) REVERT: C 1142 GLN cc_start: 0.7974 (tp40) cc_final: 0.7531 (tp40) outliers start: 74 outliers final: 58 residues processed: 633 average time/residue: 0.1794 time to fit residues: 178.5212 Evaluate side-chains 647 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 587 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 196 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 179 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 360 ASN B 30 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 675 GLN B 957 GLN C 207 HIS C 935 GLN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113954 restraints weight = 41287.687| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.49 r_work: 0.3316 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 29449 Z= 0.228 Angle : 0.702 14.528 40248 Z= 0.340 Chirality : 0.051 0.827 4723 Planarity : 0.004 0.052 5064 Dihedral : 6.414 58.425 5491 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.61 % Allowed : 18.23 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3488 helix: 1.19 (0.20), residues: 705 sheet: 0.51 (0.18), residues: 793 loop : -1.39 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.019 0.002 TYR B1067 PHE 0.043 0.002 PHE C 970 TRP 0.019 0.001 TRP A 64 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00548 (29321) covalent geometry : angle 0.64683 (39911) SS BOND : bond 0.00732 ( 47) SS BOND : angle 2.48220 ( 94) hydrogen bonds : bond 0.04654 ( 1076) hydrogen bonds : angle 5.34256 ( 3150) link_BETA1-4 : bond 0.00504 ( 28) link_BETA1-4 : angle 1.50505 ( 84) link_NAG-ASN : bond 0.00735 ( 53) link_NAG-ASN : angle 3.87124 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 583 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7895 (p0) cc_final: 0.7664 (p0) REVERT: A 95 THR cc_start: 0.8075 (m) cc_final: 0.7594 (p) REVERT: A 138 ASP cc_start: 0.7763 (m-30) cc_final: 0.7390 (m-30) REVERT: A 280 ASN cc_start: 0.7864 (t0) cc_final: 0.7625 (t0) REVERT: A 281 GLU cc_start: 0.8150 (pt0) cc_final: 0.7868 (pt0) REVERT: A 306 PHE cc_start: 0.9032 (m-80) cc_final: 0.8815 (m-10) REVERT: A 357 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7840 (ttt90) REVERT: A 414 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8017 (mm-40) REVERT: A 420 ASP cc_start: 0.7681 (m-30) cc_final: 0.7281 (t0) REVERT: A 438 SER cc_start: 0.8308 (t) cc_final: 0.7974 (t) REVERT: A 450 ASN cc_start: 0.7996 (m-40) cc_final: 0.7549 (m110) REVERT: A 484 GLU cc_start: 0.8609 (pt0) cc_final: 0.8301 (pt0) REVERT: A 803 SER cc_start: 0.8453 (t) cc_final: 0.8074 (p) REVERT: A 825 LYS cc_start: 0.8853 (ttmm) cc_final: 0.8452 (mttm) REVERT: A 979 ASP cc_start: 0.8025 (t0) cc_final: 0.7598 (t0) REVERT: B 66 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.5892 (p90) REVERT: B 188 ASN cc_start: 0.7758 (m-40) cc_final: 0.7198 (m-40) REVERT: B 207 HIS cc_start: 0.7837 (t-90) cc_final: 0.7272 (t-170) REVERT: B 281 GLU cc_start: 0.7866 (pm20) cc_final: 0.7492 (pm20) REVERT: B 378 LYS cc_start: 0.8421 (mttt) cc_final: 0.8079 (ttmm) REVERT: B 398 ASP cc_start: 0.8046 (m-30) cc_final: 0.7780 (m-30) REVERT: B 406 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7016 (mt-10) REVERT: B 484 GLU cc_start: 0.7853 (tt0) cc_final: 0.7595 (tt0) REVERT: B 571 ASP cc_start: 0.7858 (t0) cc_final: 0.7237 (t0) REVERT: B 773 GLU cc_start: 0.8068 (tt0) cc_final: 0.7827 (tt0) REVERT: B 775 ASP cc_start: 0.7987 (m-30) cc_final: 0.7762 (m-30) REVERT: B 776 LYS cc_start: 0.8370 (tttm) cc_final: 0.8057 (tptp) REVERT: B 804 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8005 (mp10) REVERT: B 882 ILE cc_start: 0.8318 (pt) cc_final: 0.8063 (mt) REVERT: B 905 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7200 (mtt180) REVERT: B 979 ASP cc_start: 0.7725 (t0) cc_final: 0.7367 (t0) REVERT: B 1072 GLU cc_start: 0.8419 (pm20) cc_final: 0.8151 (pm20) REVERT: C 158 ARG cc_start: 0.8089 (mtt90) cc_final: 0.7833 (mtt90) REVERT: C 200 TYR cc_start: 0.8059 (m-80) cc_final: 0.7633 (m-80) REVERT: C 214 ARG cc_start: 0.7516 (ptm160) cc_final: 0.7275 (ptp90) REVERT: C 316 SER cc_start: 0.8361 (p) cc_final: 0.8118 (m) REVERT: C 516 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7683 (mt-10) REVERT: C 571 ASP cc_start: 0.7863 (t0) cc_final: 0.7538 (t0) REVERT: C 772 VAL cc_start: 0.8622 (p) cc_final: 0.8375 (m) REVERT: C 796 ASP cc_start: 0.7321 (t0) cc_final: 0.6896 (t70) REVERT: C 801 ASN cc_start: 0.8005 (m-40) cc_final: 0.7755 (m-40) REVERT: C 804 GLN cc_start: 0.8394 (mt0) cc_final: 0.7961 (mp10) REVERT: C 882 ILE cc_start: 0.8349 (pt) cc_final: 0.8099 (mt) REVERT: C 1072 GLU cc_start: 0.8136 (pm20) cc_final: 0.7922 (pm20) REVERT: C 1141 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7570 (tt) REVERT: C 1142 GLN cc_start: 0.7919 (tp40) cc_final: 0.7487 (tp40) outliers start: 80 outliers final: 70 residues processed: 629 average time/residue: 0.1800 time to fit residues: 177.9277 Evaluate side-chains 651 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 578 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 196 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 248 optimal weight: 0.4980 chunk 149 optimal weight: 0.4980 chunk 257 optimal weight: 0.0870 chunk 284 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 360 ASN A 658 ASN B 30 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** L 95 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 = 0.3804 r_free = 0.3804 target = 0.140983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114969 restraints weight = 41371.302| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.50 r_work: 0.3329 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29449 Z= 0.141 Angle : 0.680 14.670 40248 Z= 0.328 Chirality : 0.050 0.802 4723 Planarity : 0.004 0.051 5064 Dihedral : 6.379 57.939 5491 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.28 % Allowed : 18.58 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3488 helix: 1.38 (0.20), residues: 687 sheet: 0.46 (0.18), residues: 792 loop : -1.31 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 357 TYR 0.016 0.001 TYR A 265 PHE 0.043 0.002 PHE C 970 TRP 0.016 0.001 TRP A 64 HIS 0.017 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00328 (29321) covalent geometry : angle 0.62323 (39911) SS BOND : bond 0.00673 ( 47) SS BOND : angle 2.61639 ( 94) hydrogen bonds : bond 0.04347 ( 1076) hydrogen bonds : angle 5.30533 ( 3150) link_BETA1-4 : bond 0.00530 ( 28) link_BETA1-4 : angle 1.50827 ( 84) link_NAG-ASN : bond 0.00803 ( 53) link_NAG-ASN : angle 3.77399 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8559.01 seconds wall clock time: 146 minutes 34.53 seconds (8794.53 seconds total)