Starting phenix.real_space_refine on Tue Jun 24 18:40:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swx_25488/06_2025/7swx_25488.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swx_25488/06_2025/7swx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7swx_25488/06_2025/7swx_25488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swx_25488/06_2025/7swx_25488.map" model { file = "/net/cci-nas-00/data/ceres_data/7swx_25488/06_2025/7swx_25488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swx_25488/06_2025/7swx_25488.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.79s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.03, per 1000 atoms: 0.63 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: 7.83 Conformation dependent library (CDL) restraints added in 3.6 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: 4.24 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: 13.32 Time building geometry restraints manager: 9.16 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 1146 or resid 1401 throu \ gh 1407)) selection = (chain 'B' and (resid 14 through 175 or resid 185 through 1146 or resid 1201 thr \ ough 1207)) selection = (chain 'C' and (resid 14 through 175 or resid 185 through 1146 or resid 1201 thr \ ough 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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 68.810 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (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 TRP 0.025 0.002 TRP H 50 HIS 0.012 0.001 HIS B1048 PHE 0.029 0.002 PHE C 377 TYR 0.028 0.001 TYR L 55 ARG 0.008 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 53) link_NAG-ASN : angle 4.25821 ( 159) link_BETA1-4 : bond 0.00748 ( 28) link_BETA1-4 : angle 2.00971 ( 84) hydrogen bonds : bond 0.17485 ( 1076) hydrogen bonds : angle 7.76701 ( 3150) SS BOND : bond 0.00349 ( 47) SS BOND : angle 1.57015 ( 94) covalent geometry : bond 0.00432 (29321) covalent geometry : angle 0.66185 (39911) *********************** 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 : 3.145 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: 0.7804 (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: 0.7491 (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: 0.8249 (t) REVERT: B 882 ILE cc_start: 0.8448 (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: 0.7828 (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: 0.7881 (mmtt) REVERT: C 558 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7905 (mtmt) REVERT: C 571 ASP cc_start: 0.7921 (t70) cc_final: 0.6987 (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: 0.7999 (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: 0.4182 time to fit residues: 412.5490 Evaluate side-chains 591 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 0.0270 chunk 264 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117264 restraints weight = 41226.278| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.53 r_work: 0.3359 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29449 Z= 0.146 Angle : 0.663 13.901 40248 Z= 0.320 Chirality : 0.048 0.450 4723 Planarity : 0.004 0.055 5064 Dihedral : 8.163 59.351 5491 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.96 % Allowed : 13.11 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 3488 helix: 1.50 (0.20), residues: 680 sheet: 0.88 (0.18), residues: 818 loop : -1.58 (0.12), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 47 HIS 0.007 0.001 HIS A 655 PHE 0.026 0.001 PHE C 970 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00834 ( 53) link_NAG-ASN : angle 3.80953 ( 159) link_BETA1-4 : bond 0.00611 ( 28) link_BETA1-4 : angle 1.71800 ( 84) hydrogen bonds : bond 0.04631 ( 1076) hydrogen bonds : angle 6.09079 ( 3150) SS BOND : bond 0.00431 ( 47) SS BOND : angle 2.17675 ( 94) covalent geometry : bond 0.00333 (29321) covalent geometry : angle 0.60622 (39911) *********************** 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 671 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 611 time to evaluate : 3.177 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 52 GLN cc_start: 0.8844 (tt0) cc_final: 0.8553 (tt0) REVERT: A 95 THR cc_start: 0.8180 (m) cc_final: 0.7762 (p) REVERT: A 191 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7887 (mt-10) REVERT: A 266 TYR cc_start: 0.8633 (m-80) cc_final: 0.8343 (m-80) REVERT: A 306 PHE cc_start: 0.8985 (m-80) cc_final: 0.8698 (m-10) REVERT: A 450 ASN cc_start: 0.7934 (m-40) cc_final: 0.7439 (m110) REVERT: A 516 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 695 TYR cc_start: 0.7913 (p90) cc_final: 0.7090 (p90) REVERT: A 949 GLN cc_start: 0.8522 (mm110) cc_final: 0.8082 (mm-40) REVERT: B 28 TYR cc_start: 0.8251 (m-80) cc_final: 0.8038 (m-80) REVERT: B 66 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6272 (p-80) REVERT: B 153 MET cc_start: 0.6886 (mmm) cc_final: 0.6670 (mmm) REVERT: B 188 ASN cc_start: 0.7657 (m-40) cc_final: 0.7196 (m-40) REVERT: B 281 GLU cc_start: 0.7921 (pm20) cc_final: 0.7587 (pm20) REVERT: B 373 SER cc_start: 0.8212 (p) cc_final: 0.7911 (t) REVERT: B 377 PHE cc_start: 0.8531 (t80) cc_final: 0.8282 (t80) REVERT: B 378 LYS cc_start: 0.8267 (mttt) cc_final: 0.7904 (ttmm) REVERT: B 398 ASP cc_start: 0.8018 (m-30) cc_final: 0.7764 (m-30) REVERT: B 571 ASP cc_start: 0.7746 (t0) cc_final: 0.7341 (t0) REVERT: B 714 ILE cc_start: 0.8116 (mm) cc_final: 0.7886 (mt) REVERT: B 747 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7528 (t) REVERT: B 882 ILE cc_start: 0.8385 (pt) cc_final: 0.8058 (mt) REVERT: B 979 ASP cc_start: 0.7739 (t70) cc_final: 0.7284 (t0) REVERT: C 66 HIS cc_start: 0.7607 (m-70) cc_final: 0.7345 (m170) REVERT: C 81 ASN cc_start: 0.8312 (p0) cc_final: 0.8105 (p0) REVERT: C 96 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6987 (mt-10) REVERT: C 158 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7725 (mtt90) REVERT: C 200 TYR cc_start: 0.7971 (m-80) cc_final: 0.7667 (m-80) REVERT: C 296 LEU cc_start: 0.7651 (tp) cc_final: 0.7371 (tt) REVERT: C 304 LYS cc_start: 0.8179 (mmtp) cc_final: 0.7969 (mptt) REVERT: C 430 THR cc_start: 0.7800 (m) cc_final: 0.7247 (p) REVERT: C 440 ASN cc_start: 0.7975 (m110) cc_final: 0.7733 (m110) REVERT: C 458 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8175 (mtpt) REVERT: C 495 TYR cc_start: 0.7727 (m-80) cc_final: 0.7205 (m-80) REVERT: C 529 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7938 (mmtt) REVERT: C 558 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7976 (mtmt) REVERT: C 571 ASP cc_start: 0.8046 (t70) cc_final: 0.7159 (t0) REVERT: C 578 ASP cc_start: 0.7626 (t0) cc_final: 0.7404 (t0) REVERT: C 772 VAL cc_start: 0.8634 (p) cc_final: 0.8383 (m) REVERT: C 797 PHE cc_start: 0.7872 (m-80) cc_final: 0.7182 (m-80) REVERT: C 1005 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8041 (tp40) REVERT: C 1055 SER cc_start: 0.8760 (m) cc_final: 0.8501 (t) REVERT: C 1072 GLU cc_start: 0.8037 (pm20) cc_final: 0.7677 (pm20) REVERT: C 1141 LEU cc_start: 0.8073 (tt) cc_final: 0.7835 (tt) outliers start: 60 outliers final: 36 residues processed: 640 average time/residue: 0.4149 time to fit residues: 416.3740 Evaluate side-chains 598 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 560 time to evaluate : 2.914 ------------------------------------------------------------------------------- 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 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 670 ILE Chi-restraints excluded: chain A residue 779 GLN 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 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 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 227 VAL Chi-restraints excluded: chain C residue 298 GLU 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 976 VAL Chi-restraints excluded: chain C residue 1073 LYS 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 154 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 336 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 580 GLN B 501 ASN B 613 GLN B 901 GLN C 207 HIS 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 = 0.3784 r_free = 0.3784 target = 0.139223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113022 restraints weight = 41295.214| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.49 r_work: 0.3304 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 29449 Z= 0.284 Angle : 0.735 15.077 40248 Z= 0.360 Chirality : 0.051 0.416 4723 Planarity : 0.005 0.058 5064 Dihedral : 7.655 59.580 5491 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.16 % Allowed : 14.12 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 3488 helix: 1.10 (0.20), residues: 681 sheet: 0.66 (0.18), residues: 783 loop : -1.57 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.008 0.001 HIS A 207 PHE 0.026 0.002 PHE C1121 TYR 0.031 0.002 TYR B 204 ARG 0.008 0.001 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00963 ( 53) link_NAG-ASN : angle 3.66028 ( 159) link_BETA1-4 : bond 0.00637 ( 28) link_BETA1-4 : angle 1.63821 ( 84) hydrogen bonds : bond 0.05397 ( 1076) hydrogen bonds : angle 5.88248 ( 3150) SS BOND : bond 0.00840 ( 47) SS BOND : angle 2.60993 ( 94) covalent geometry : bond 0.00673 (29321) covalent geometry : angle 0.68499 (39911) *********************** 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 698 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 601 time to evaluate : 3.217 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 40 ASP cc_start: 0.7221 (p0) cc_final: 0.6997 (p0) REVERT: A 61 ASN cc_start: 0.7763 (t0) cc_final: 0.7556 (m-40) REVERT: A 95 THR cc_start: 0.8269 (m) cc_final: 0.7804 (p) REVERT: A 266 TYR cc_start: 0.8594 (m-80) cc_final: 0.8311 (m-80) REVERT: A 414 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8016 (mm-40) REVERT: A 420 ASP cc_start: 0.7685 (m-30) cc_final: 0.7320 (t0) REVERT: A 450 ASN cc_start: 0.8012 (m-40) cc_final: 0.7552 (m110) REVERT: A 516 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 695 TYR cc_start: 0.8211 (p90) cc_final: 0.7449 (p90) REVERT: A 803 SER cc_start: 0.8466 (t) cc_final: 0.8094 (p) REVERT: A 804 GLN cc_start: 0.8539 (mm-40) cc_final: 0.7935 (mm-40) REVERT: A 904 TYR cc_start: 0.8056 (m-10) cc_final: 0.7784 (m-80) REVERT: A 979 ASP cc_start: 0.7992 (t0) cc_final: 0.7628 (t0) REVERT: A 1114 ILE cc_start: 0.8069 (mt) cc_final: 0.7864 (mm) REVERT: A 1130 ILE cc_start: 0.8213 (pt) cc_final: 0.7742 (mt) REVERT: B 188 ASN cc_start: 0.7826 (m-40) cc_final: 0.7370 (m-40) REVERT: B 281 GLU cc_start: 0.7875 (pm20) cc_final: 0.7537 (pm20) REVERT: B 373 SER cc_start: 0.8199 (p) cc_final: 0.7969 (t) REVERT: B 376 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7932 (p) REVERT: B 378 LYS cc_start: 0.8436 (mttt) cc_final: 0.8080 (ttmm) REVERT: B 571 ASP cc_start: 0.7854 (t0) cc_final: 0.7392 (t0) REVERT: B 747 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7519 (t) REVERT: B 905 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7072 (mtt180) REVERT: B 979 ASP cc_start: 0.7760 (t70) cc_final: 0.7344 (t0) REVERT: C 30 ASN cc_start: 0.8157 (t0) cc_final: 0.7954 (t0) REVERT: C 132 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 158 ARG cc_start: 0.8033 (mtt90) cc_final: 0.7512 (mtt90) REVERT: C 304 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7987 (mptt) REVERT: C 430 THR cc_start: 0.7877 (m) cc_final: 0.7488 (p) REVERT: C 440 ASN cc_start: 0.8043 (m110) cc_final: 0.7809 (m110) REVERT: C 529 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7919 (mmtt) REVERT: C 558 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7964 (mtmt) REVERT: C 772 VAL cc_start: 0.8690 (p) cc_final: 0.8450 (m) REVERT: C 796 ASP cc_start: 0.7437 (t0) cc_final: 0.7046 (t70) REVERT: C 801 ASN cc_start: 0.7879 (m-40) cc_final: 0.7664 (m-40) REVERT: C 804 GLN cc_start: 0.8368 (mt0) cc_final: 0.8034 (mp10) REVERT: C 954 GLN cc_start: 0.8291 (mt0) cc_final: 0.8074 (mt0) REVERT: C 1072 GLU cc_start: 0.8102 (pm20) cc_final: 0.7691 (pm20) REVERT: C 1139 ASP cc_start: 0.7935 (t0) cc_final: 0.7713 (t0) REVERT: C 1141 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7691 (tt) REVERT: C 1142 GLN cc_start: 0.7805 (mp10) cc_final: 0.7381 (mp10) outliers start: 97 outliers final: 64 residues processed: 652 average time/residue: 0.4161 time to fit residues: 425.7720 Evaluate side-chains 631 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 564 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 549 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 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 101 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL 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 516 GLU 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 747 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP 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 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 180 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 316 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 321 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 580 GLN A 658 ASN A1106 GLN B 30 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN C 949 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 = 0.3809 r_free = 0.3809 target = 0.141163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115052 restraints weight = 41597.794| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.52 r_work: 0.3335 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1696 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 : 0.675 22.704 40248 Z= 0.322 Chirality : 0.047 0.378 4723 Planarity : 0.004 0.054 5064 Dihedral : 7.139 57.764 5491 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.28 % Allowed : 15.85 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3488 helix: 1.37 (0.20), residues: 680 sheet: 0.74 (0.18), residues: 768 loop : -1.48 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.010 0.001 HIS B 207 PHE 0.016 0.001 PHE A1121 TYR 0.017 0.001 TYR B1067 ARG 0.005 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00791 ( 53) link_NAG-ASN : angle 4.17344 ( 159) link_BETA1-4 : bond 0.00644 ( 28) link_BETA1-4 : angle 1.50305 ( 84) hydrogen bonds : bond 0.04287 ( 1076) hydrogen bonds : angle 5.56066 ( 3150) SS BOND : bond 0.00625 ( 47) SS BOND : angle 2.42298 ( 94) covalent geometry : bond 0.00322 (29321) covalent geometry : angle 0.60906 (39911) *********************** 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 658 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 588 time to evaluate : 3.143 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: A 40 ASP cc_start: 0.7291 (p0) cc_final: 0.7051 (p0) REVERT: A 95 THR cc_start: 0.8221 (m) cc_final: 0.7757 (p) REVERT: A 138 ASP cc_start: 0.7244 (t0) cc_final: 0.6940 (p0) REVERT: A 169 GLU cc_start: 0.7740 (tp30) cc_final: 0.7528 (tp30) REVERT: A 280 ASN cc_start: 0.7925 (t0) cc_final: 0.7675 (t0) REVERT: A 281 GLU cc_start: 0.8133 (pt0) cc_final: 0.7912 (pt0) REVERT: A 306 PHE cc_start: 0.9055 (m-80) cc_final: 0.8767 (m-10) REVERT: A 414 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7978 (mm-40) REVERT: A 438 SER cc_start: 0.8375 (t) cc_final: 0.8006 (t) REVERT: A 450 ASN cc_start: 0.7988 (m-40) cc_final: 0.7520 (m110) REVERT: A 516 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 695 TYR cc_start: 0.8196 (p90) cc_final: 0.7404 (p90) REVERT: A 803 SER cc_start: 0.8407 (t) cc_final: 0.8056 (p) REVERT: A 825 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8587 (mttm) REVERT: A 979 ASP cc_start: 0.8010 (t0) cc_final: 0.7609 (t0) REVERT: A 1114 ILE cc_start: 0.8113 (mt) cc_final: 0.7895 (mm) REVERT: B 188 ASN cc_start: 0.7772 (m-40) cc_final: 0.7254 (m-40) REVERT: B 281 GLU cc_start: 0.7864 (pm20) cc_final: 0.7489 (pm20) REVERT: B 373 SER cc_start: 0.8202 (p) cc_final: 0.7929 (t) REVERT: B 378 LYS cc_start: 0.8430 (mttt) cc_final: 0.8089 (ttmm) REVERT: B 571 ASP cc_start: 0.7812 (t0) cc_final: 0.7314 (t0) REVERT: B 804 GLN cc_start: 0.8257 (mm110) cc_final: 0.7974 (mp10) REVERT: B 905 ARG cc_start: 0.7540 (mtt180) cc_final: 0.6938 (mtt180) REVERT: B 979 ASP cc_start: 0.7729 (t70) cc_final: 0.7269 (t0) REVERT: C 53 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7754 (t0) REVERT: C 132 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7205 (mt-10) REVERT: C 158 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7572 (mtt90) REVERT: C 200 TYR cc_start: 0.7956 (m-80) cc_final: 0.7632 (m-80) REVERT: C 304 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7919 (mptt) REVERT: C 440 ASN cc_start: 0.8012 (m110) cc_final: 0.7772 (m110) REVERT: C 529 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7927 (mmtt) REVERT: C 558 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7965 (mtmt) REVERT: C 571 ASP cc_start: 0.8031 (t0) cc_final: 0.7654 (t0) REVERT: C 772 VAL cc_start: 0.8622 (p) cc_final: 0.8382 (m) REVERT: C 801 ASN cc_start: 0.7796 (m-40) cc_final: 0.7574 (m-40) REVERT: C 804 GLN cc_start: 0.8260 (mt0) cc_final: 0.7970 (mp10) REVERT: C 868 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: C 1072 GLU cc_start: 0.8120 (pm20) cc_final: 0.7721 (pm20) REVERT: C 1141 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7693 (tt) outliers start: 70 outliers final: 48 residues processed: 627 average time/residue: 0.4220 time to fit residues: 413.8586 Evaluate side-chains 619 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 568 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 108 THR 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 340 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 399 SER 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 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 949 GLN Chi-restraints excluded: chain A residue 1028 LYS 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 143 VAL Chi-restraints excluded: chain B residue 334 ASN 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 896 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR 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 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 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 868 GLU 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 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 248 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 162 optimal weight: 0.3980 chunk 181 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 258 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 307 optimal weight: 6.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 580 GLN A1101 HIS B 30 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN B 675 GLN ** B 762 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113209 restraints weight = 41534.360| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.50 r_work: 0.3309 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 29449 Z= 0.251 Angle : 0.714 15.109 40248 Z= 0.345 Chirality : 0.050 0.592 4723 Planarity : 0.005 0.056 5064 Dihedral : 6.976 58.075 5491 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.26 % Allowed : 16.07 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3488 helix: 1.22 (0.20), residues: 681 sheet: 0.62 (0.18), residues: 791 loop : -1.50 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.009 0.001 HIS C 207 PHE 0.022 0.002 PHE A1089 TYR 0.024 0.002 TYR B 204 ARG 0.007 0.001 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 53) link_NAG-ASN : angle 4.10139 ( 159) link_BETA1-4 : bond 0.00510 ( 28) link_BETA1-4 : angle 1.49522 ( 84) hydrogen bonds : bond 0.04943 ( 1076) hydrogen bonds : angle 5.59734 ( 3150) SS BOND : bond 0.00813 ( 47) SS BOND : angle 2.71478 ( 94) covalent geometry : bond 0.00599 (29321) covalent geometry : angle 0.65189 (39911) *********************** 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 684 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 584 time to evaluate : 3.404 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 40 ASP cc_start: 0.7319 (p0) cc_final: 0.7039 (p0) REVERT: A 81 ASN cc_start: 0.7863 (p0) cc_final: 0.7556 (p0) REVERT: A 95 THR cc_start: 0.8207 (m) cc_final: 0.7729 (p) REVERT: A 198 ASP cc_start: 0.7479 (t0) cc_final: 0.7256 (t70) REVERT: A 266 TYR cc_start: 0.8622 (m-80) cc_final: 0.8323 (m-80) REVERT: A 280 ASN cc_start: 0.7885 (t0) cc_final: 0.7621 (t0) REVERT: A 281 GLU cc_start: 0.8160 (pt0) cc_final: 0.7938 (pt0) REVERT: A 306 PHE cc_start: 0.9083 (m-80) cc_final: 0.8827 (m-10) REVERT: A 414 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7946 (mm-40) REVERT: A 420 ASP cc_start: 0.7661 (m-30) cc_final: 0.7176 (t0) REVERT: A 450 ASN cc_start: 0.8022 (m-40) cc_final: 0.7572 (m110) REVERT: A 484 GLU cc_start: 0.8624 (pt0) cc_final: 0.8301 (pt0) REVERT: A 516 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7301 (mm-30) REVERT: A 660 TYR cc_start: 0.8354 (m-10) cc_final: 0.8101 (m-10) REVERT: A 666 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7690 (mt) REVERT: A 803 SER cc_start: 0.8469 (t) cc_final: 0.8089 (p) REVERT: A 825 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8557 (mttm) REVERT: A 904 TYR cc_start: 0.8050 (m-10) cc_final: 0.7783 (m-80) REVERT: A 979 ASP cc_start: 0.7962 (t0) cc_final: 0.7521 (t0) REVERT: A 1114 ILE cc_start: 0.8129 (mt) cc_final: 0.7910 (mm) REVERT: B 188 ASN cc_start: 0.7823 (m-40) cc_final: 0.7247 (m-40) REVERT: B 281 GLU cc_start: 0.7879 (pm20) cc_final: 0.7513 (pm20) REVERT: B 324 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7622 (mt-10) REVERT: B 373 SER cc_start: 0.8162 (p) cc_final: 0.7940 (t) REVERT: B 376 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7971 (p) REVERT: B 378 LYS cc_start: 0.8352 (mttt) cc_final: 0.8013 (ttmm) REVERT: B 484 GLU cc_start: 0.7850 (tt0) cc_final: 0.7580 (tt0) REVERT: B 571 ASP cc_start: 0.7829 (t0) cc_final: 0.7292 (t0) REVERT: B 882 ILE cc_start: 0.8394 (pt) cc_final: 0.8064 (mt) REVERT: B 902 MET cc_start: 0.7670 (tpp) cc_final: 0.7447 (tpp) REVERT: B 945 LEU cc_start: 0.8455 (mt) cc_final: 0.8169 (mp) REVERT: B 979 ASP cc_start: 0.7758 (t70) cc_final: 0.7374 (t0) REVERT: B 1119 ASN cc_start: 0.6730 (OUTLIER) cc_final: 0.6262 (m-40) REVERT: C 132 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7301 (mt-10) REVERT: C 158 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7506 (mtt90) REVERT: C 304 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7974 (mptt) REVERT: C 516 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7813 (mt-10) REVERT: C 529 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7914 (mmtt) REVERT: C 571 ASP cc_start: 0.8023 (t0) cc_final: 0.7790 (t0) REVERT: C 772 VAL cc_start: 0.8641 (p) cc_final: 0.8405 (m) REVERT: C 796 ASP cc_start: 0.7419 (t0) cc_final: 0.7059 (t70) REVERT: C 801 ASN cc_start: 0.7911 (m-40) cc_final: 0.7647 (m-40) REVERT: C 804 GLN cc_start: 0.8333 (mt0) cc_final: 0.8014 (mp10) REVERT: C 868 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: C 1072 GLU cc_start: 0.8128 (pm20) cc_final: 0.7559 (pm20) REVERT: C 1141 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7709 (tt) outliers start: 100 outliers final: 77 residues processed: 638 average time/residue: 0.4210 time to fit residues: 423.1383 Evaluate side-chains 656 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 574 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 108 THR 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 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 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 666 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR 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 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 143 VAL Chi-restraints excluded: chain B residue 153 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 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 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 45 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 324 GLU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 393 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 534 VAL 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 791 THR Chi-restraints excluded: chain C residue 868 GLU 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 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 263 optimal weight: 4.9990 chunk 255 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 284 optimal weight: 0.0040 chunk 259 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 580 GLN A 658 ASN A 935 GLN A1083 HIS B 30 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN C 949 GLN 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 = 0.3800 r_free = 0.3800 target = 0.140616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114414 restraints weight = 41500.767| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.51 r_work: 0.3325 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 29449 Z= 0.163 Angle : 0.667 15.085 40248 Z= 0.322 Chirality : 0.048 0.648 4723 Planarity : 0.004 0.055 5064 Dihedral : 6.716 57.857 5491 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.13 % Allowed : 16.60 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3488 helix: 1.40 (0.20), residues: 681 sheet: 0.61 (0.18), residues: 781 loop : -1.42 (0.12), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.007 0.001 HIS B 207 PHE 0.034 0.001 PHE A 140 TYR 0.017 0.001 TYR A 265 ARG 0.007 0.000 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 53) link_NAG-ASN : angle 3.74166 ( 159) link_BETA1-4 : bond 0.00525 ( 28) link_BETA1-4 : angle 1.49783 ( 84) hydrogen bonds : bond 0.04374 ( 1076) hydrogen bonds : angle 5.44698 ( 3150) SS BOND : bond 0.00703 ( 47) SS BOND : angle 2.63422 ( 94) covalent geometry : bond 0.00385 (29321) covalent geometry : angle 0.61017 (39911) *********************** 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 684 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 588 time to evaluate : 3.209 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 40 ASP cc_start: 0.7314 (p0) cc_final: 0.7082 (p0) REVERT: A 81 ASN cc_start: 0.7833 (p0) cc_final: 0.7591 (p0) REVERT: A 95 THR cc_start: 0.8134 (m) cc_final: 0.7673 (p) REVERT: A 169 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7171 (tp30) REVERT: A 266 TYR cc_start: 0.8571 (m-80) cc_final: 0.8351 (m-80) REVERT: A 280 ASN cc_start: 0.7859 (t0) cc_final: 0.7607 (t0) REVERT: A 281 GLU cc_start: 0.8188 (pt0) cc_final: 0.7944 (pt0) REVERT: A 306 PHE cc_start: 0.9059 (m-80) cc_final: 0.8803 (m-10) REVERT: A 414 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7995 (mm-40) REVERT: A 420 ASP cc_start: 0.7692 (m-30) cc_final: 0.7224 (t0) REVERT: A 438 SER cc_start: 0.8305 (t) cc_final: 0.7969 (t) REVERT: A 450 ASN cc_start: 0.7998 (m-40) cc_final: 0.7554 (m110) REVERT: A 484 GLU cc_start: 0.8641 (pt0) cc_final: 0.8372 (pt0) REVERT: A 666 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 695 TYR cc_start: 0.8309 (p90) cc_final: 0.7521 (p90) REVERT: A 803 SER cc_start: 0.8428 (t) cc_final: 0.8052 (p) REVERT: A 825 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8559 (mttm) REVERT: A 979 ASP cc_start: 0.8007 (t0) cc_final: 0.7556 (t0) REVERT: A 1114 ILE cc_start: 0.8143 (mt) cc_final: 0.7929 (mm) REVERT: B 188 ASN cc_start: 0.7771 (m-40) cc_final: 0.7199 (m-40) REVERT: B 281 GLU cc_start: 0.7878 (pm20) cc_final: 0.7487 (pm20) REVERT: B 373 SER cc_start: 0.8148 (p) cc_final: 0.7922 (t) REVERT: B 376 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7982 (p) REVERT: B 378 LYS cc_start: 0.8444 (mttt) cc_final: 0.8106 (ttmm) REVERT: B 398 ASP cc_start: 0.8047 (m-30) cc_final: 0.7730 (m-30) REVERT: B 484 GLU cc_start: 0.7887 (tt0) cc_final: 0.7639 (tt0) REVERT: B 571 ASP cc_start: 0.7826 (t0) cc_final: 0.7283 (t0) REVERT: B 654 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 804 GLN cc_start: 0.8208 (mm110) cc_final: 0.7946 (mp10) REVERT: B 882 ILE cc_start: 0.8386 (pt) cc_final: 0.8080 (mt) REVERT: B 905 ARG cc_start: 0.7538 (mtt180) cc_final: 0.6967 (mtt180) REVERT: B 945 LEU cc_start: 0.8508 (mt) cc_final: 0.8231 (mp) REVERT: B 955 ASN cc_start: 0.7820 (m-40) cc_final: 0.7608 (t0) REVERT: B 979 ASP cc_start: 0.7729 (t70) cc_final: 0.7300 (t0) REVERT: C 158 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7533 (mtt90) REVERT: C 290 ASP cc_start: 0.7984 (t0) cc_final: 0.7778 (t0) REVERT: C 516 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7754 (mt-10) REVERT: C 529 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7914 (mmtt) REVERT: C 571 ASP cc_start: 0.8121 (t0) cc_final: 0.7890 (t0) REVERT: C 772 VAL cc_start: 0.8631 (p) cc_final: 0.8379 (m) REVERT: C 801 ASN cc_start: 0.7967 (m-40) cc_final: 0.7721 (m-40) REVERT: C 804 GLN cc_start: 0.8276 (mt0) cc_final: 0.7993 (mp10) REVERT: C 868 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: C 1072 GLU cc_start: 0.8113 (pm20) cc_final: 0.7858 (pm20) REVERT: C 1141 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7663 (tt) outliers start: 96 outliers final: 71 residues processed: 639 average time/residue: 0.4377 time to fit residues: 441.2581 Evaluate side-chains 646 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 570 time to evaluate : 3.024 ------------------------------------------------------------------------------- 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 53 ASP 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 169 GLU Chi-restraints excluded: chain A residue 259 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 399 SER 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 666 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 949 GLN 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 45 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL 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 516 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 990 GLU 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 308 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 393 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 534 VAL Chi-restraints excluded: chain C residue 569 ILE 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 868 GLU 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 H residue 12 VAL 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 240 optimal weight: 5.9990 chunk 326 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 99 ASN A 314 GLN A 658 ASN B 30 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN B 955 ASN B1011 GLN 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 = 0.3807 r_free = 0.3807 target = 0.141191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115040 restraints weight = 41356.922| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.51 r_work: 0.3333 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2169 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= 0.152 Angle : 0.662 14.976 40248 Z= 0.320 Chirality : 0.048 0.841 4723 Planarity : 0.004 0.054 5064 Dihedral : 6.470 57.850 5491 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.33 % Allowed : 16.99 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3488 helix: 1.44 (0.20), residues: 687 sheet: 0.61 (0.18), residues: 766 loop : -1.36 (0.12), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.007 0.001 HIS B 207 PHE 0.040 0.001 PHE C 970 TYR 0.017 0.001 TYR A 265 ARG 0.007 0.000 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 53) link_NAG-ASN : angle 3.54671 ( 159) link_BETA1-4 : bond 0.00510 ( 28) link_BETA1-4 : angle 1.48700 ( 84) hydrogen bonds : bond 0.04208 ( 1076) hydrogen bonds : angle 5.31504 ( 3150) SS BOND : bond 0.00648 ( 47) SS BOND : angle 2.66975 ( 94) covalent geometry : bond 0.00359 (29321) covalent geometry : angle 0.60849 (39911) *********************** 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 703 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 601 time to evaluate : 3.255 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 40 ASP cc_start: 0.7332 (p0) cc_final: 0.7097 (p0) REVERT: A 81 ASN cc_start: 0.7891 (p0) cc_final: 0.7625 (p0) REVERT: A 95 THR cc_start: 0.8074 (m) cc_final: 0.7604 (p) REVERT: A 280 ASN cc_start: 0.7845 (t0) cc_final: 0.7597 (t0) REVERT: A 281 GLU cc_start: 0.8159 (pt0) cc_final: 0.7886 (pt0) REVERT: A 306 PHE cc_start: 0.9045 (m-80) cc_final: 0.8794 (m-10) REVERT: A 357 ARG cc_start: 0.8094 (ttt90) cc_final: 0.7874 (ttt90) REVERT: A 414 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8021 (mm-40) REVERT: A 420 ASP cc_start: 0.7709 (m-30) cc_final: 0.7239 (t0) REVERT: A 438 SER cc_start: 0.8305 (t) cc_final: 0.7964 (t) REVERT: A 450 ASN cc_start: 0.7983 (m-40) cc_final: 0.7566 (m110) REVERT: A 695 TYR cc_start: 0.8231 (p90) cc_final: 0.7464 (p90) REVERT: A 803 SER cc_start: 0.8412 (t) cc_final: 0.8039 (p) REVERT: A 825 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8560 (mttm) REVERT: A 979 ASP cc_start: 0.8024 (t0) cc_final: 0.7577 (t0) REVERT: A 1114 ILE cc_start: 0.8142 (mt) cc_final: 0.7942 (mm) REVERT: B 188 ASN cc_start: 0.7744 (m-40) cc_final: 0.7298 (m-40) REVERT: B 207 HIS cc_start: 0.7932 (t-170) cc_final: 0.7656 (t-170) REVERT: B 281 GLU cc_start: 0.7869 (pm20) cc_final: 0.7493 (pm20) REVERT: B 376 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7970 (p) REVERT: B 378 LYS cc_start: 0.8409 (mttt) cc_final: 0.8081 (ttmm) REVERT: B 398 ASP cc_start: 0.8040 (m-30) cc_final: 0.7709 (m-30) REVERT: B 406 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: B 484 GLU cc_start: 0.7857 (tt0) cc_final: 0.7596 (tt0) REVERT: B 571 ASP cc_start: 0.7834 (t0) cc_final: 0.7294 (t0) REVERT: B 654 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 703 ASN cc_start: 0.8197 (t0) cc_final: 0.7445 (m-40) REVERT: B 804 GLN cc_start: 0.8226 (mm110) cc_final: 0.7971 (mp10) REVERT: B 882 ILE cc_start: 0.8349 (pt) cc_final: 0.8083 (mt) REVERT: B 945 LEU cc_start: 0.8487 (mt) cc_final: 0.8224 (mp) REVERT: B 978 ASN cc_start: 0.8223 (m-40) cc_final: 0.7921 (m-40) REVERT: B 979 ASP cc_start: 0.7727 (t0) cc_final: 0.7314 (t0) REVERT: C 158 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7486 (mtt90) REVERT: C 200 TYR cc_start: 0.7931 (m-80) cc_final: 0.7641 (m-80) REVERT: C 290 ASP cc_start: 0.7989 (t0) cc_final: 0.7786 (t0) REVERT: C 516 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7764 (mt-10) REVERT: C 571 ASP cc_start: 0.8127 (t0) cc_final: 0.7874 (t0) REVERT: C 772 VAL cc_start: 0.8621 (p) cc_final: 0.8369 (m) REVERT: C 796 ASP cc_start: 0.7357 (t0) cc_final: 0.6934 (t70) REVERT: C 801 ASN cc_start: 0.7963 (m-40) cc_final: 0.7723 (m-40) REVERT: C 804 GLN cc_start: 0.8260 (mt0) cc_final: 0.7990 (mp10) REVERT: C 894 LEU cc_start: 0.8067 (mt) cc_final: 0.7808 (mp) REVERT: C 1072 GLU cc_start: 0.8150 (pm20) cc_final: 0.7881 (pm20) REVERT: C 1141 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7672 (tt) REVERT: C 1142 GLN cc_start: 0.7948 (tp40) cc_final: 0.7539 (tp40) outliers start: 102 outliers final: 74 residues processed: 659 average time/residue: 0.4337 time to fit residues: 451.2909 Evaluate side-chains 660 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 583 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS 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 166 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 299 THR 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 588 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 949 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1038 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 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 324 GLU 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 445 VAL 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 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 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 45 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 324 GLU 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 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 654 GLU 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 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 112 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 113 optimal weight: 0.5980 chunk 288 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 275 optimal weight: 0.5980 chunk 155 optimal weight: 0.0870 chunk 281 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 245 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 99 ASN A 580 GLN A 658 ASN A 764 ASN B 30 ASN B 137 ASN B 613 GLN B 957 GLN 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 = 0.3817 r_free = 0.3817 target = 0.141968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115832 restraints weight = 41590.841| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.53 r_work: 0.3343 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29449 Z= 0.119 Angle : 0.638 18.800 40248 Z= 0.306 Chirality : 0.048 0.998 4723 Planarity : 0.004 0.053 5064 Dihedral : 6.273 57.845 5491 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.48 % Allowed : 18.26 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3488 helix: 1.42 (0.20), residues: 711 sheet: 0.68 (0.18), residues: 764 loop : -1.30 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.007 0.001 HIS B 207 PHE 0.030 0.001 PHE C 970 TYR 0.018 0.001 TYR A 265 ARG 0.007 0.000 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 53) link_NAG-ASN : angle 3.55915 ( 159) link_BETA1-4 : bond 0.00508 ( 28) link_BETA1-4 : angle 1.46445 ( 84) hydrogen bonds : bond 0.03815 ( 1076) hydrogen bonds : angle 5.17136 ( 3150) SS BOND : bond 0.00645 ( 47) SS BOND : angle 2.31255 ( 94) covalent geometry : bond 0.00274 (29321) covalent geometry : angle 0.58537 (39911) *********************** 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 674 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 598 time to evaluate : 3.146 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 40 ASP cc_start: 0.7325 (p0) cc_final: 0.7099 (p0) REVERT: A 81 ASN cc_start: 0.7875 (p0) cc_final: 0.7611 (p0) REVERT: A 95 THR cc_start: 0.8035 (m) cc_final: 0.7577 (p) REVERT: A 132 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6441 (tt0) REVERT: A 280 ASN cc_start: 0.7831 (t0) cc_final: 0.7576 (t0) REVERT: A 281 GLU cc_start: 0.8165 (pt0) cc_final: 0.7873 (pt0) REVERT: A 306 PHE cc_start: 0.9026 (m-80) cc_final: 0.8781 (m-10) REVERT: A 357 ARG cc_start: 0.8101 (ttt90) cc_final: 0.7846 (ttt90) REVERT: A 414 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8007 (mm-40) REVERT: A 420 ASP cc_start: 0.7714 (m-30) cc_final: 0.7235 (t0) REVERT: A 438 SER cc_start: 0.8381 (t) cc_final: 0.7996 (t) REVERT: A 450 ASN cc_start: 0.7979 (m-40) cc_final: 0.7561 (m110) REVERT: A 803 SER cc_start: 0.8379 (t) cc_final: 0.8015 (p) REVERT: A 825 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8543 (mttm) REVERT: A 979 ASP cc_start: 0.8015 (t0) cc_final: 0.7584 (t0) REVERT: A 1114 ILE cc_start: 0.8133 (mt) cc_final: 0.7931 (mm) REVERT: B 188 ASN cc_start: 0.7688 (m-40) cc_final: 0.7247 (m-40) REVERT: B 207 HIS cc_start: 0.7895 (t-170) cc_final: 0.7618 (t-170) REVERT: B 281 GLU cc_start: 0.7864 (pm20) cc_final: 0.7454 (pm20) REVERT: B 376 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7986 (p) REVERT: B 378 LYS cc_start: 0.8369 (mttt) cc_final: 0.8037 (ttmm) REVERT: B 398 ASP cc_start: 0.8048 (m-30) cc_final: 0.7698 (m-30) REVERT: B 484 GLU cc_start: 0.7839 (tt0) cc_final: 0.7600 (tt0) REVERT: B 571 ASP cc_start: 0.7818 (t0) cc_final: 0.7240 (t0) REVERT: B 643 PHE cc_start: 0.8219 (t80) cc_final: 0.7728 (t80) REVERT: B 703 ASN cc_start: 0.8184 (t0) cc_final: 0.7414 (m-40) REVERT: B 804 GLN cc_start: 0.8167 (mm110) cc_final: 0.7939 (mp10) REVERT: B 882 ILE cc_start: 0.8310 (pt) cc_final: 0.8083 (mt) REVERT: B 979 ASP cc_start: 0.7690 (t0) cc_final: 0.7272 (t0) REVERT: B 1017 GLU cc_start: 0.7804 (tt0) cc_final: 0.7591 (tt0) REVERT: B 1075 PHE cc_start: 0.8504 (m-80) cc_final: 0.8271 (m-80) REVERT: C 132 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7213 (mt-10) REVERT: C 158 ARG cc_start: 0.8047 (mtt90) cc_final: 0.7463 (mtt90) REVERT: C 516 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 571 ASP cc_start: 0.8024 (t0) cc_final: 0.7774 (t0) REVERT: C 660 TYR cc_start: 0.8272 (m-10) cc_final: 0.7664 (m-80) REVERT: C 772 VAL cc_start: 0.8623 (p) cc_final: 0.8360 (m) REVERT: C 801 ASN cc_start: 0.7958 (m-40) cc_final: 0.7708 (m-40) REVERT: C 804 GLN cc_start: 0.8212 (mt0) cc_final: 0.7972 (mp10) REVERT: C 957 GLN cc_start: 0.8652 (tt0) cc_final: 0.8397 (tt0) REVERT: C 1037 SER cc_start: 0.8082 (t) cc_final: 0.7809 (p) REVERT: C 1072 GLU cc_start: 0.8151 (pm20) cc_final: 0.7866 (pm20) REVERT: C 1141 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7659 (tt) REVERT: C 1142 GLN cc_start: 0.7969 (tp40) cc_final: 0.7528 (tp40) outliers start: 76 outliers final: 60 residues processed: 640 average time/residue: 0.4082 time to fit residues: 410.8244 Evaluate side-chains 646 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 584 time to evaluate : 3.247 ------------------------------------------------------------------------------- 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 153 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 299 THR 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 588 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 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 41 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 45 SER 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 302 THR Chi-restraints excluded: chain C residue 308 VAL 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 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 637 SER 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 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 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 116 optimal weight: 3.9990 chunk 233 optimal weight: 0.0870 chunk 81 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 257 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 280 optimal weight: 0.3980 chunk 253 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 207 HIS A 658 ASN B 30 ASN B 501 ASN B 613 GLN B 655 HIS ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3819 r_free = 0.3819 target = 0.142233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116050 restraints weight = 41422.857| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.52 r_work: 0.3341 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29449 Z= 0.121 Angle : 0.640 15.008 40248 Z= 0.308 Chirality : 0.049 1.095 4723 Planarity : 0.004 0.053 5064 Dihedral : 6.144 57.885 5491 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.54 % Allowed : 18.39 % Favored : 79.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3488 helix: 1.57 (0.20), residues: 695 sheet: 0.71 (0.18), residues: 762 loop : -1.23 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.007 0.001 HIS B 207 PHE 0.028 0.001 PHE C 970 TYR 0.017 0.001 TYR A 265 ARG 0.007 0.000 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 53) link_NAG-ASN : angle 3.51063 ( 159) link_BETA1-4 : bond 0.00488 ( 28) link_BETA1-4 : angle 1.48204 ( 84) hydrogen bonds : bond 0.03780 ( 1076) hydrogen bonds : angle 5.12265 ( 3150) SS BOND : bond 0.00675 ( 47) SS BOND : angle 2.30001 ( 94) covalent geometry : bond 0.00282 (29321) covalent geometry : angle 0.58949 (39911) *********************** 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 670 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 592 time to evaluate : 3.243 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 40 ASP cc_start: 0.7339 (p0) cc_final: 0.7122 (p0) REVERT: A 81 ASN cc_start: 0.7886 (p0) cc_final: 0.7628 (p0) REVERT: A 95 THR cc_start: 0.8047 (m) cc_final: 0.7586 (p) REVERT: A 132 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6433 (tt0) REVERT: A 280 ASN cc_start: 0.7789 (t0) cc_final: 0.7541 (t0) REVERT: A 281 GLU cc_start: 0.8144 (pt0) cc_final: 0.7852 (pt0) REVERT: A 306 PHE cc_start: 0.9019 (m-80) cc_final: 0.8761 (m-10) REVERT: A 357 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7847 (ttt90) REVERT: A 414 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7933 (mm110) REVERT: A 420 ASP cc_start: 0.7700 (m-30) cc_final: 0.7215 (t0) REVERT: A 438 SER cc_start: 0.8308 (t) cc_final: 0.7957 (t) REVERT: A 450 ASN cc_start: 0.7971 (m-40) cc_final: 0.7573 (m110) REVERT: A 803 SER cc_start: 0.8361 (t) cc_final: 0.7998 (p) REVERT: A 825 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8540 (mttm) REVERT: A 979 ASP cc_start: 0.8015 (t0) cc_final: 0.7620 (t0) REVERT: A 1114 ILE cc_start: 0.8133 (mt) cc_final: 0.7933 (mm) REVERT: A 1132 ILE cc_start: 0.8274 (tt) cc_final: 0.8035 (tp) REVERT: B 188 ASN cc_start: 0.7674 (m-40) cc_final: 0.7226 (m-40) REVERT: B 207 HIS cc_start: 0.7872 (t-170) cc_final: 0.7606 (t-170) REVERT: B 281 GLU cc_start: 0.7863 (pm20) cc_final: 0.7445 (pm20) REVERT: B 377 PHE cc_start: 0.8453 (t80) cc_final: 0.8185 (t80) REVERT: B 378 LYS cc_start: 0.8464 (mttt) cc_final: 0.8144 (ttmm) REVERT: B 398 ASP cc_start: 0.8023 (m-30) cc_final: 0.7685 (m-30) REVERT: B 484 GLU cc_start: 0.7900 (tt0) cc_final: 0.7635 (tt0) REVERT: B 489 TYR cc_start: 0.7777 (m-80) cc_final: 0.7405 (m-80) REVERT: B 571 ASP cc_start: 0.7838 (t0) cc_final: 0.7233 (t0) REVERT: B 643 PHE cc_start: 0.8243 (t80) cc_final: 0.7896 (t80) REVERT: B 655 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8296 (t-90) REVERT: B 703 ASN cc_start: 0.8178 (t0) cc_final: 0.7424 (m-40) REVERT: B 775 ASP cc_start: 0.8083 (m-30) cc_final: 0.7851 (m-30) REVERT: B 804 GLN cc_start: 0.8162 (mm110) cc_final: 0.7949 (mp10) REVERT: B 882 ILE cc_start: 0.8319 (pt) cc_final: 0.8090 (mt) REVERT: B 979 ASP cc_start: 0.7710 (t0) cc_final: 0.7362 (t0) REVERT: C 131 CYS cc_start: 0.6466 (m) cc_final: 0.6099 (m) REVERT: C 158 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7547 (mtt90) REVERT: C 516 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 571 ASP cc_start: 0.8050 (t0) cc_final: 0.7782 (t0) REVERT: C 660 TYR cc_start: 0.8309 (m-10) cc_final: 0.7661 (m-80) REVERT: C 772 VAL cc_start: 0.8640 (p) cc_final: 0.8380 (m) REVERT: C 801 ASN cc_start: 0.7968 (m-40) cc_final: 0.7712 (m-40) REVERT: C 804 GLN cc_start: 0.8200 (mt0) cc_final: 0.7897 (mp10) REVERT: C 957 GLN cc_start: 0.8621 (tt0) cc_final: 0.8339 (tt0) REVERT: C 1037 SER cc_start: 0.8069 (t) cc_final: 0.7655 (p) REVERT: C 1072 GLU cc_start: 0.8163 (pm20) cc_final: 0.7866 (pm20) REVERT: C 1106 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8050 (pt0) REVERT: C 1141 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7591 (tt) REVERT: C 1142 GLN cc_start: 0.7977 (tp40) cc_final: 0.7548 (tp40) outliers start: 78 outliers final: 60 residues processed: 636 average time/residue: 0.4382 time to fit residues: 441.8360 Evaluate side-chains 654 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 591 time to evaluate : 2.918 ------------------------------------------------------------------------------- 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 153 MET Chi-restraints excluded: chain A residue 259 THR 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 553 THR Chi-restraints excluded: chain A residue 588 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 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 41 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 655 HIS 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 990 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 45 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 302 THR Chi-restraints excluded: chain C residue 308 VAL 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 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 637 SER 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 1073 LYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1106 GLN 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 339 optimal weight: 40.0000 chunk 214 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 chunk 299 optimal weight: 0.4980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 207 HIS A 580 GLN A 658 ASN B 30 ASN ** B 655 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.141529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114195 restraints weight = 41552.498| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.70 r_work: 0.3323 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2390 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= 0.162 Angle : 0.665 14.986 40248 Z= 0.320 Chirality : 0.050 1.046 4723 Planarity : 0.004 0.054 5064 Dihedral : 6.203 57.770 5491 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.25 % Allowed : 18.78 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3488 helix: 1.45 (0.20), residues: 695 sheet: 0.69 (0.18), residues: 764 loop : -1.23 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 258 HIS 0.008 0.001 HIS A 207 PHE 0.029 0.001 PHE C 970 TYR 0.017 0.001 TYR B1067 ARG 0.010 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00682 ( 53) link_NAG-ASN : angle 3.58698 ( 159) link_BETA1-4 : bond 0.00481 ( 28) link_BETA1-4 : angle 1.49341 ( 84) hydrogen bonds : bond 0.04060 ( 1076) hydrogen bonds : angle 5.16160 ( 3150) SS BOND : bond 0.00700 ( 47) SS BOND : angle 2.36397 ( 94) covalent geometry : bond 0.00384 (29321) covalent geometry : angle 0.61435 (39911) ********************** 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 660 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 591 time to evaluate : 3.058 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 40 ASP cc_start: 0.7328 (p0) cc_final: 0.7122 (p0) REVERT: A 81 ASN cc_start: 0.7928 (p0) cc_final: 0.7694 (p0) REVERT: A 95 THR cc_start: 0.8101 (m) cc_final: 0.7656 (p) REVERT: A 280 ASN cc_start: 0.7840 (t0) cc_final: 0.7601 (t0) REVERT: A 281 GLU cc_start: 0.8195 (pt0) cc_final: 0.7906 (pt0) REVERT: A 298 GLU cc_start: 0.7940 (tt0) cc_final: 0.7602 (tt0) REVERT: A 357 ARG cc_start: 0.8118 (ttt90) cc_final: 0.7884 (ttt90) REVERT: A 414 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7979 (mm110) REVERT: A 420 ASP cc_start: 0.7749 (m-30) cc_final: 0.7277 (t0) REVERT: A 438 SER cc_start: 0.8400 (t) cc_final: 0.8086 (t) REVERT: A 450 ASN cc_start: 0.7966 (m-40) cc_final: 0.7576 (m110) REVERT: A 803 SER cc_start: 0.8416 (t) cc_final: 0.8059 (p) REVERT: A 825 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8574 (mttm) REVERT: A 979 ASP cc_start: 0.8085 (t0) cc_final: 0.7659 (t0) REVERT: A 1132 ILE cc_start: 0.8357 (tt) cc_final: 0.8132 (tp) REVERT: B 188 ASN cc_start: 0.7700 (m-40) cc_final: 0.7258 (m-40) REVERT: B 207 HIS cc_start: 0.7919 (t-170) cc_final: 0.7659 (t-170) REVERT: B 281 GLU cc_start: 0.7859 (pm20) cc_final: 0.7464 (pm20) REVERT: B 377 PHE cc_start: 0.8460 (t80) cc_final: 0.8176 (t80) REVERT: B 378 LYS cc_start: 0.8509 (mttt) cc_final: 0.8211 (ttmm) REVERT: B 398 ASP cc_start: 0.8024 (m-30) cc_final: 0.7682 (m-30) REVERT: B 406 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: B 484 GLU cc_start: 0.7946 (tt0) cc_final: 0.7676 (tt0) REVERT: B 489 TYR cc_start: 0.7782 (m-80) cc_final: 0.7449 (m-80) REVERT: B 571 ASP cc_start: 0.7852 (t0) cc_final: 0.7284 (t0) REVERT: B 643 PHE cc_start: 0.8285 (t80) cc_final: 0.8055 (t80) REVERT: B 703 ASN cc_start: 0.8223 (t0) cc_final: 0.7465 (m-40) REVERT: B 804 GLN cc_start: 0.8263 (mm110) cc_final: 0.8017 (mp10) REVERT: B 882 ILE cc_start: 0.8388 (pt) cc_final: 0.8159 (mt) REVERT: B 945 LEU cc_start: 0.8517 (mm) cc_final: 0.8216 (mp) REVERT: B 979 ASP cc_start: 0.7795 (t0) cc_final: 0.7377 (t0) REVERT: C 131 CYS cc_start: 0.6630 (m) cc_final: 0.6320 (m) REVERT: C 158 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7540 (mtt90) REVERT: C 516 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7841 (mt-10) REVERT: C 571 ASP cc_start: 0.7990 (t0) cc_final: 0.7717 (t0) REVERT: C 660 TYR cc_start: 0.8291 (m-10) cc_final: 0.7560 (m-80) REVERT: C 772 VAL cc_start: 0.8673 (p) cc_final: 0.8436 (m) REVERT: C 801 ASN cc_start: 0.8070 (m-40) cc_final: 0.7807 (m-40) REVERT: C 804 GLN cc_start: 0.8355 (mt0) cc_final: 0.7961 (mp10) REVERT: C 957 GLN cc_start: 0.8720 (tt0) cc_final: 0.8438 (tt0) REVERT: C 1037 SER cc_start: 0.8097 (t) cc_final: 0.7800 (p) REVERT: C 1072 GLU cc_start: 0.8235 (pm20) cc_final: 0.7930 (pm20) REVERT: C 1106 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: C 1141 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7610 (tt) REVERT: C 1142 GLN cc_start: 0.8027 (tp40) cc_final: 0.7585 (tp40) outliers start: 69 outliers final: 63 residues processed: 629 average time/residue: 0.4138 time to fit residues: 408.2597 Evaluate side-chains 651 residues out of total 3067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 585 time to evaluate : 2.805 ------------------------------------------------------------------------------- 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 153 MET Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 259 THR 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 399 SER Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR 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 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 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 597 VAL 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 990 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 45 SER 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 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 534 VAL Chi-restraints excluded: chain C residue 582 LEU 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 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 1106 GLN 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 152 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 33 optimal weight: 0.0040 chunk 271 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 207 HIS A 658 ASN B 30 ASN B 655 HIS B 804 GLN B 901 GLN B 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 = 0.3790 r_free = 0.3790 target = 0.140004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113287 restraints weight = 41472.567| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.63 r_work: 0.3298 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29449 Z= 0.215 Angle : 0.691 15.151 40248 Z= 0.336 Chirality : 0.051 0.969 4723 Planarity : 0.004 0.054 5064 Dihedral : 6.229 57.869 5491 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.51 % Allowed : 18.75 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3488 helix: 1.34 (0.20), residues: 687 sheet: 0.59 (0.18), residues: 773 loop : -1.24 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.020 0.001 HIS A 207 PHE 0.029 0.002 PHE C 970 TYR 0.018 0.002 TYR B1067 ARG 0.008 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 53) link_NAG-ASN : angle 3.49414 ( 159) link_BETA1-4 : bond 0.00449 ( 28) link_BETA1-4 : angle 1.47012 ( 84) hydrogen bonds : bond 0.04513 ( 1076) hydrogen bonds : angle 5.29095 ( 3150) SS BOND : bond 0.00756 ( 47) SS BOND : angle 2.50948 ( 94) covalent geometry : bond 0.00512 (29321) covalent geometry : angle 0.64342 (39911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18690.85 seconds wall clock time: 321 minutes 37.75 seconds (19297.75 seconds total)