Starting phenix.real_space_refine on Fri Mar 6 13:21:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7df4_30661/03_2026/7df4_30661.cif Found real_map, /net/cci-nas-00/data/ceres_data/7df4_30661/03_2026/7df4_30661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7df4_30661/03_2026/7df4_30661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7df4_30661/03_2026/7df4_30661.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7df4_30661/03_2026/7df4_30661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7df4_30661/03_2026/7df4_30661.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.073 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 145 5.16 5 C 19663 2.51 5 N 5062 2.21 5 O 6050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30920 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "C" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8332 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 52, 'TRANS': 1012} Chain breaks: 5 Chain: "B" Number of atoms: 8355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8355 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 5 Chain: "D" Number of atoms: 8355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8355 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.77, per 1000 atoms: 0.22 Number of scatterers: 30920 At special positions: 0 Unit cell: (159.12, 151.98, 235.62, 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 145 16.00 O 6050 8.00 N 5062 7.00 C 19663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 234 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 122 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 17 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 149 " " NAG C1309 " - " ASN C 122 " " NAG C1310 " - " ASN C 61 " " NAG C1311 " - " ASN C 17 " " NAG D1301 " - " ASN D 709 " " NAG D1302 " - " ASN D 657 " " NAG D1303 " - " ASN D 616 " " NAG D1304 " - " ASN D 603 " " NAG D1305 " - " ASN D 343 " " NAG D1306 " - " ASN D 331 " " NAG D1307 " - " ASN D 282 " " NAG D1308 " - " ASN D 234 " " NAG D1309 " - " ASN D 165 " " NAG D1310 " - " ASN D 149 " " NAG D1311 " - " ASN D 122 " " NAG D1312 " - " ASN D 61 " " NAG D1313 " - " ASN D 17 " " NAG E 1 " - " ASN C1134 " " NAG F 1 " - " ASN C1098 " " NAG G 1 " - " ASN C1074 " " NAG H 1 " - " ASN C 801 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 709 " " NAG K 1 " - " ASN C 282 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN D1134 " " NAG S 1 " - " ASN D1098 " " NAG T 1 " - " ASN D1074 " " NAG U 1 " - " ASN D 801 " " NAG V 1 " - " ASN D 717 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7130 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 52 sheets defined 30.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.826A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.826A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.227A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.611A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.625A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.823A pdb=" N LYS A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.591A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 252 removed outlier: 4.161A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.769A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.546A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.772A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.633A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.329A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 398 through 413 removed outlier: 4.737A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.585A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.265A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.866A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.713A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.534A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.549A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 365 through 371 removed outlier: 4.182A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.638A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.063A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.757A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.644A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.507A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.716A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 854 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 910 removed outlier: 3.555A pdb=" N PHE C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.750A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.520A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (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 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.822A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.962A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.553A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.288A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) 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 removed outlier: 3.531A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.818A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 4.492A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.845A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 removed outlier: 4.034A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.550A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.827A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.729A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.895A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 removed outlier: 3.693A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.646A pdb=" N THR D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 removed outlier: 4.130A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.015A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 410 removed outlier: 3.991A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 782 Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.500A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 897 through 910 removed outlier: 3.540A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.693A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.685A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.199A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.793A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP D1146 " --> pdb=" O GLN D1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.692A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.220A pdb=" N ALA A 348 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 359 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP A 350 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG A 357 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 352 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.585A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AA6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.640A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.607A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.607A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.546A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.759A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.504A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.639A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.803A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 701 through 704 removed outlier: 3.517A pdb=" N LYS D 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.841A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.667A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.192A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 787 through 790 removed outlier: 5.447A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC4, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.939A pdb=" N PHE B 43 " --> pdb=" O ARG D 567 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.509A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.610A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.541A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.502A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.740A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.505A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.048A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.536A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 653 through 656 removed outlier: 5.664A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.707A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.474A pdb=" N ILE B 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.570A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 224 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.540A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR D 274 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP D 290 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 276 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA D 288 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.539A pdb=" N GLY D 142 " --> pdb=" O GLU D 156 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 156 " --> pdb=" O GLY D 142 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 84 through 85 removed outlier: 7.517A pdb=" N ARG D 237 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE D 106 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN D 239 " --> pdb=" O TRP D 104 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP D 104 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU D 241 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 311 through 317 removed outlier: 7.138A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.692A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 402 " --> pdb=" O TYR D 508 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 436 " --> pdb=" O ARG D 509 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 511 " --> pdb=" O ILE D 434 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 434 " --> pdb=" O VAL D 511 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'D' and resid 654 through 656 removed outlier: 5.746A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 711 through 715 removed outlier: 3.761A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.541A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'D' and resid 1094 through 1097 1152 hydrogen bonds defined for protein. 3228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9181 1.34 - 1.46: 6812 1.46 - 1.58: 15442 1.58 - 1.70: 2 1.70 - 1.83: 196 Bond restraints: 31633 Sorted by residual: bond pdb=" C GLN D 271 " pdb=" N PRO D 272 " ideal model delta sigma weight residual 1.334 1.467 -0.133 2.34e-02 1.83e+03 3.24e+01 bond pdb=" C1 NAG S 1 " pdb=" C2 NAG S 1 " ideal model delta sigma weight residual 1.532 1.634 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C PRO C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 1.334 1.451 -0.117 2.34e-02 1.83e+03 2.49e+01 bond pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " ideal model delta sigma weight residual 1.532 1.631 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C PRO D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.334 1.442 -0.108 2.34e-02 1.83e+03 2.13e+01 ... (remaining 31628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 42481 2.33 - 4.66: 504 4.66 - 6.99: 25 6.99 - 9.32: 12 9.32 - 11.65: 5 Bond angle restraints: 43027 Sorted by residual: angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 108.84 116.13 -7.29 1.32e+00 5.74e-01 3.05e+01 angle pdb=" N ASN D 149 " pdb=" CA ASN D 149 " pdb=" C ASN D 149 " ideal model delta sigma weight residual 110.80 102.11 8.69 2.13e+00 2.20e-01 1.67e+01 angle pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 110.06 98.41 11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C6 NAG Q 2 " pdb=" C5 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 108.73 120.35 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C2 NAG S 1 " pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 110.06 98.84 11.22 3.00e+00 1.11e-01 1.40e+01 ... (remaining 43022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 19170 15.84 - 31.69: 416 31.69 - 47.53: 132 47.53 - 63.37: 36 63.37 - 79.22: 2 Dihedral angle restraints: 19756 sinusoidal: 8681 harmonic: 11075 Sorted by residual: dihedral pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" N GLY A 147 " pdb=" CA GLY A 147 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN C 149 " pdb=" C ASN C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual 180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASN B 149 " pdb=" C ASN B 149 " pdb=" N LYS B 150 " pdb=" CA LYS B 150 " ideal model delta harmonic sigma weight residual 180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 19753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 4967 0.165 - 0.331: 40 0.331 - 0.496: 6 0.496 - 0.662: 1 0.662 - 0.827: 4 Chirality restraints: 5018 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-02 2.50e+03 1.34e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-02 2.50e+03 1.13e+03 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 -2.13 -0.27 2.00e-02 2.50e+03 1.78e+02 ... (remaining 5015 not shown) Planarity restraints: 5535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG G 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.352 2.00e-02 2.50e+03 3.01e-01 1.14e+03 pdb=" C7 NAG J 1 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.535 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.324 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG F 1 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.504 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.181 2.00e-02 2.50e+03 ... (remaining 5532 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 12 2.19 - 2.87: 10793 2.87 - 3.55: 41667 3.55 - 4.22: 74948 4.22 - 4.90: 124000 Nonbonded interactions: 251420 Sorted by model distance: nonbonded pdb=" O SER B 704 " pdb=" C8 NAG N 2 " model vdw 1.519 3.460 nonbonded pdb=" OG1 THR D1100 " pdb=" C1 NAG S 1 " model vdw 1.593 3.470 nonbonded pdb=" OG1 THR C1100 " pdb=" C1 NAG F 1 " model vdw 1.594 3.470 nonbonded pdb=" O ASN D 122 " pdb=" OE2 GLU D 154 " model vdw 1.947 3.040 nonbonded pdb=" O ASN C 343 " pdb=" OD1 ASN C 343 " model vdw 2.000 3.040 ... (remaining 251415 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 'B' and (resid 16 through 827 or resid 849 through 1311)) selection = chain 'C' selection = (chain 'D' and (resid 16 through 827 or resid 849 through 1311)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.780 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 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 0.237 31748 Z= 0.225 Angle : 0.642 21.031 43327 Z= 0.308 Chirality : 0.055 0.827 5018 Planarity : 0.017 0.305 5481 Dihedral : 7.933 79.218 12500 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 0.21 % Allowed : 0.24 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.11), residues: 3760 helix: -2.81 (0.11), residues: 970 sheet: -1.12 (0.15), residues: 736 loop : -1.05 (0.12), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1039 TYR 0.019 0.001 TYR B 495 PHE 0.013 0.001 PHE B 32 TRP 0.020 0.001 TRP C 64 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00352 (31633) covalent geometry : angle 0.57204 (43027) SS BOND : bond 0.00164 ( 42) SS BOND : angle 0.89851 ( 84) hydrogen bonds : bond 0.28624 ( 1149) hydrogen bonds : angle 10.19141 ( 3228) Misc. bond : bond 0.23728 ( 1) link_BETA1-4 : bond 0.00706 ( 18) link_BETA1-4 : angle 3.62924 ( 54) link_NAG-ASN : bond 0.01227 ( 54) link_NAG-ASN : angle 4.28814 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1043 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 360 MET cc_start: 0.4330 (ttp) cc_final: 0.4067 (ptm) REVERT: C 54 LEU cc_start: 0.8273 (mt) cc_final: 0.7883 (mt) REVERT: C 90 VAL cc_start: 0.7508 (t) cc_final: 0.6962 (p) REVERT: C 240 THR cc_start: 0.7748 (m) cc_final: 0.7181 (p) REVERT: C 271 GLN cc_start: 0.8500 (mt0) cc_final: 0.7792 (mp10) REVERT: C 296 LEU cc_start: 0.8534 (tp) cc_final: 0.8285 (tt) REVERT: C 380 TYR cc_start: 0.5635 (m-10) cc_final: 0.5432 (m-10) REVERT: C 400 PHE cc_start: 0.7356 (p90) cc_final: 0.6941 (p90) REVERT: C 505 TYR cc_start: 0.4174 (m-80) cc_final: 0.3930 (m-80) REVERT: C 596 SER cc_start: 0.8476 (m) cc_final: 0.7882 (p) REVERT: C 611 LEU cc_start: 0.9451 (tp) cc_final: 0.9092 (tt) REVERT: C 698 SER cc_start: 0.8410 (t) cc_final: 0.7688 (p) REVERT: C 729 VAL cc_start: 0.9431 (t) cc_final: 0.9190 (m) REVERT: C 730 SER cc_start: 0.8378 (t) cc_final: 0.8161 (p) REVERT: C 740 MET cc_start: 0.6832 (mtp) cc_final: 0.6536 (mtp) REVERT: C 752 LEU cc_start: 0.8852 (mt) cc_final: 0.8556 (mp) REVERT: C 775 ASP cc_start: 0.7379 (m-30) cc_final: 0.7078 (m-30) REVERT: C 788 ILE cc_start: 0.7877 (mt) cc_final: 0.7632 (mm) REVERT: C 882 ILE cc_start: 0.7341 (mt) cc_final: 0.6990 (mt) REVERT: C 913 GLN cc_start: 0.8421 (pt0) cc_final: 0.7912 (pm20) REVERT: C 933 LYS cc_start: 0.8366 (mttt) cc_final: 0.7894 (tptt) REVERT: C 962 LEU cc_start: 0.8880 (tp) cc_final: 0.8632 (tp) REVERT: B 22 THR cc_start: 0.6027 (m) cc_final: 0.5732 (t) REVERT: B 51 THR cc_start: 0.6929 (t) cc_final: 0.6674 (t) REVERT: B 106 PHE cc_start: 0.5604 (m-10) cc_final: 0.5070 (m-80) REVERT: B 201 PHE cc_start: 0.5531 (t80) cc_final: 0.5090 (t80) REVERT: B 302 THR cc_start: 0.8720 (m) cc_final: 0.8503 (t) REVERT: B 342 PHE cc_start: 0.5437 (t80) cc_final: 0.5020 (t80) REVERT: B 451 TYR cc_start: 0.3452 (m-10) cc_final: 0.3210 (m-10) REVERT: B 500 THR cc_start: 0.5345 (p) cc_final: 0.4730 (t) REVERT: B 517 LEU cc_start: 0.6322 (tp) cc_final: 0.6117 (tp) REVERT: B 563 GLN cc_start: 0.6323 (mt0) cc_final: 0.5998 (mp10) REVERT: B 697 MET cc_start: 0.7688 (ttt) cc_final: 0.7445 (ttp) REVERT: B 737 ASP cc_start: 0.7712 (t0) cc_final: 0.7334 (t0) REVERT: B 751 ASN cc_start: 0.8336 (m-40) cc_final: 0.7260 (m110) REVERT: B 752 LEU cc_start: 0.8683 (mt) cc_final: 0.7755 (mt) REVERT: B 778 THR cc_start: 0.8062 (p) cc_final: 0.7793 (p) REVERT: B 780 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7502 (mm-30) REVERT: B 854 LYS cc_start: 0.5443 (ttpt) cc_final: 0.4992 (tmmt) REVERT: B 872 GLN cc_start: 0.7693 (mt0) cc_final: 0.7307 (tp-100) REVERT: B 931 ILE cc_start: 0.9186 (mm) cc_final: 0.8916 (mt) REVERT: B 950 ASP cc_start: 0.7622 (m-30) cc_final: 0.7359 (m-30) REVERT: B 955 ASN cc_start: 0.8419 (m-40) cc_final: 0.8033 (t0) REVERT: B 960 ASN cc_start: 0.8003 (m-40) cc_final: 0.7601 (t0) REVERT: B 979 ASP cc_start: 0.7853 (m-30) cc_final: 0.7548 (t0) REVERT: B 994 ASP cc_start: 0.7672 (t70) cc_final: 0.7126 (m-30) REVERT: B 1029 MET cc_start: 0.8463 (tpp) cc_final: 0.8083 (tpp) REVERT: B 1045 LYS cc_start: 0.7903 (tttt) cc_final: 0.7327 (mttt) REVERT: B 1105 THR cc_start: 0.8534 (p) cc_final: 0.7944 (p) REVERT: B 1125 ASN cc_start: 0.7997 (p0) cc_final: 0.7693 (m-40) REVERT: D 267 VAL cc_start: 0.7904 (t) cc_final: 0.7663 (t) REVERT: D 396 TYR cc_start: 0.5773 (m-80) cc_final: 0.4904 (m-10) REVERT: D 398 ASP cc_start: 0.5261 (m-30) cc_final: 0.4986 (m-30) REVERT: D 664 ILE cc_start: 0.9293 (mt) cc_final: 0.9056 (mt) REVERT: D 673 SER cc_start: 0.8318 (t) cc_final: 0.7934 (m) REVERT: D 730 SER cc_start: 0.8689 (t) cc_final: 0.7982 (p) REVERT: D 737 ASP cc_start: 0.7874 (t0) cc_final: 0.7406 (p0) REVERT: D 761 THR cc_start: 0.8592 (m) cc_final: 0.8357 (p) REVERT: D 804 GLN cc_start: 0.7585 (mp10) cc_final: 0.7112 (mp10) REVERT: D 875 SER cc_start: 0.8669 (t) cc_final: 0.8466 (m) REVERT: D 902 MET cc_start: 0.8592 (mmm) cc_final: 0.8307 (mmt) REVERT: D 974 SER cc_start: 0.8473 (t) cc_final: 0.8085 (p) REVERT: D 1047 TYR cc_start: 0.8624 (m-80) cc_final: 0.8344 (m-80) outliers start: 7 outliers final: 3 residues processed: 1049 average time/residue: 0.1913 time to fit residues: 320.5141 Evaluate side-chains 537 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 534 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 1133 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.0470 overall best weight: 1.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS A 401 HIS A 417 HIS A 540 HIS A 599 ASN C 137 ASN C 188 ASN C 409 GLN C 481 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 536 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN C1119 ASN B 52 GLN B 66 HIS B 125 ASN B 207 HIS B 317 ASN B 388 ASN B 644 GLN B 655 HIS B 675 GLN B 774 GLN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1101 HIS B1106 GLN D 69 HIS D 188 ASN D 196 ASN D 239 GLN D 321 GLN D 394 ASN D 481 ASN D 519 HIS ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN D 965 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.136129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.116591 restraints weight = 119333.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.117570 restraints weight = 83503.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.118107 restraints weight = 53237.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.118138 restraints weight = 48758.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.118317 restraints weight = 43862.819| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31748 Z= 0.248 Angle : 0.842 18.460 43327 Z= 0.408 Chirality : 0.052 0.388 5018 Planarity : 0.005 0.053 5481 Dihedral : 7.155 59.060 5588 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 3.40 % Allowed : 9.17 % Favored : 87.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.12), residues: 3760 helix: -0.76 (0.15), residues: 1014 sheet: -0.76 (0.16), residues: 711 loop : -1.04 (0.12), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 983 TYR 0.025 0.003 TYR B 904 PHE 0.034 0.003 PHE B 201 TRP 0.036 0.003 TRP C 64 HIS 0.007 0.002 HIS D1064 Details of bonding type rmsd covalent geometry : bond 0.00539 (31633) covalent geometry : angle 0.79218 (43027) SS BOND : bond 0.00803 ( 42) SS BOND : angle 2.73100 ( 84) hydrogen bonds : bond 0.05957 ( 1149) hydrogen bonds : angle 6.91078 ( 3228) Misc. bond : bond 0.01805 ( 1) link_BETA1-4 : bond 0.01698 ( 18) link_BETA1-4 : angle 4.09430 ( 54) link_NAG-ASN : bond 0.00642 ( 54) link_NAG-ASN : angle 3.69375 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 564 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.5645 (t80) cc_final: 0.5021 (t80) REVERT: A 45 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.4839 (mt) REVERT: A 168 TRP cc_start: 0.1350 (t-100) cc_final: 0.0234 (t60) REVERT: A 360 MET cc_start: 0.4764 (ttp) cc_final: 0.4023 (ptm) REVERT: A 428 PHE cc_start: 0.5629 (m-80) cc_final: 0.5296 (m-80) REVERT: A 474 MET cc_start: 0.3405 (tpp) cc_final: 0.3146 (tpp) REVERT: A 592 PHE cc_start: 0.3647 (t80) cc_final: 0.3446 (t80) REVERT: C 240 THR cc_start: 0.7590 (m) cc_final: 0.7336 (p) REVERT: C 270 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6571 (tp) REVERT: C 380 TYR cc_start: 0.5875 (m-80) cc_final: 0.5095 (m-10) REVERT: C 614 ASP cc_start: 0.6372 (t0) cc_final: 0.6032 (t0) REVERT: C 698 SER cc_start: 0.8496 (t) cc_final: 0.7967 (p) REVERT: C 756 TYR cc_start: 0.7457 (m-10) cc_final: 0.7200 (m-10) REVERT: C 774 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8362 (mm110) REVERT: C 775 ASP cc_start: 0.7091 (m-30) cc_final: 0.6697 (m-30) REVERT: C 780 GLU cc_start: 0.7429 (pt0) cc_final: 0.6679 (pt0) REVERT: C 878 LEU cc_start: 0.9014 (mt) cc_final: 0.8629 (mt) REVERT: C 965 GLN cc_start: 0.7834 (mm110) cc_final: 0.7445 (mt0) REVERT: C 993 ILE cc_start: 0.8651 (pt) cc_final: 0.8361 (pt) REVERT: B 106 PHE cc_start: 0.5744 (m-10) cc_final: 0.5456 (m-80) REVERT: B 452 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6613 (mt) REVERT: B 500 THR cc_start: 0.5665 (p) cc_final: 0.5156 (t) REVERT: B 707 TYR cc_start: 0.7212 (t80) cc_final: 0.6925 (t80) REVERT: B 731 MET cc_start: 0.8519 (ttp) cc_final: 0.8068 (ptm) REVERT: B 789 TYR cc_start: 0.8558 (m-80) cc_final: 0.8300 (m-80) REVERT: B 931 ILE cc_start: 0.8805 (mm) cc_final: 0.8579 (mt) REVERT: B 950 ASP cc_start: 0.6454 (m-30) cc_final: 0.6247 (m-30) REVERT: B 1029 MET cc_start: 0.8552 (tpp) cc_final: 0.8324 (tpp) REVERT: D 304 LYS cc_start: 0.8091 (mttt) cc_final: 0.7488 (tttt) REVERT: D 321 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.4735 (pt0) REVERT: D 353 TRP cc_start: 0.6973 (OUTLIER) cc_final: 0.6649 (p-90) REVERT: D 394 ASN cc_start: 0.5033 (OUTLIER) cc_final: 0.4572 (t160) REVERT: D 902 MET cc_start: 0.8479 (mmm) cc_final: 0.8022 (mmt) REVERT: D 973 ILE cc_start: 0.7732 (tp) cc_final: 0.7470 (mm) REVERT: D 1003 SER cc_start: 0.9264 (p) cc_final: 0.9008 (m) REVERT: D 1028 LYS cc_start: 0.8153 (mttt) cc_final: 0.7847 (mttt) REVERT: D 1030 SER cc_start: 0.9024 (m) cc_final: 0.8574 (m) outliers start: 113 outliers final: 69 residues processed: 638 average time/residue: 0.1836 time to fit residues: 191.5805 Evaluate side-chains 505 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 430 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 925 ASN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 353 TRP Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 939 SER Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1133 VAL Chi-restraints excluded: chain D residue 1146 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 317 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 343 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 74 optimal weight: 0.0030 chunk 160 optimal weight: 0.9980 chunk 324 optimal weight: 6.9990 chunk 347 optimal weight: 0.0050 chunk 17 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 125 ASN C 173 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 856 ASN B 901 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.136837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.117763 restraints weight = 119087.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.118362 restraints weight = 96793.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.118813 restraints weight = 62523.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.118975 restraints weight = 55465.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.119096 restraints weight = 50208.973| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 31748 Z= 0.147 Angle : 0.701 19.137 43327 Z= 0.342 Chirality : 0.047 0.325 5018 Planarity : 0.004 0.062 5481 Dihedral : 6.569 58.241 5584 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 2.74 % Allowed : 11.76 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.12), residues: 3760 helix: -0.14 (0.15), residues: 1019 sheet: -0.53 (0.17), residues: 693 loop : -0.99 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 115 TYR 0.024 0.002 TYR C 365 PHE 0.023 0.002 PHE C 817 TRP 0.033 0.002 TRP B 886 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00310 (31633) covalent geometry : angle 0.65230 (43027) SS BOND : bond 0.00356 ( 42) SS BOND : angle 3.12356 ( 84) hydrogen bonds : bond 0.05079 ( 1149) hydrogen bonds : angle 6.37334 ( 3228) Misc. bond : bond 0.00411 ( 1) link_BETA1-4 : bond 0.01239 ( 18) link_BETA1-4 : angle 3.88693 ( 54) link_NAG-ASN : bond 0.00570 ( 54) link_NAG-ASN : angle 2.90584 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 509 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.5510 (t80) cc_final: 0.4847 (t80) REVERT: A 45 LEU cc_start: 0.5452 (OUTLIER) cc_final: 0.4827 (mt) REVERT: A 168 TRP cc_start: 0.1344 (t-100) cc_final: 0.0199 (t60) REVERT: A 190 MET cc_start: 0.3275 (ptp) cc_final: 0.3072 (ttt) REVERT: A 360 MET cc_start: 0.4677 (ttp) cc_final: 0.4040 (ptm) REVERT: A 428 PHE cc_start: 0.5668 (m-80) cc_final: 0.5334 (m-80) REVERT: A 593 THR cc_start: 0.6711 (m) cc_final: 0.6364 (t) REVERT: C 240 THR cc_start: 0.7494 (m) cc_final: 0.7285 (p) REVERT: C 614 ASP cc_start: 0.6260 (t0) cc_final: 0.5767 (t0) REVERT: C 698 SER cc_start: 0.8518 (t) cc_final: 0.8015 (p) REVERT: C 756 TYR cc_start: 0.7384 (m-10) cc_final: 0.7071 (m-10) REVERT: C 775 ASP cc_start: 0.6939 (m-30) cc_final: 0.6701 (m-30) REVERT: C 864 LEU cc_start: 0.8485 (tp) cc_final: 0.8280 (tt) REVERT: C 865 LEU cc_start: 0.8729 (mp) cc_final: 0.8375 (mt) REVERT: C 959 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8301 (mp) REVERT: C 962 LEU cc_start: 0.8851 (tp) cc_final: 0.8383 (tp) REVERT: C 965 GLN cc_start: 0.7765 (mm110) cc_final: 0.7442 (mm-40) REVERT: B 452 LEU cc_start: 0.6970 (mp) cc_final: 0.6769 (mt) REVERT: B 500 THR cc_start: 0.5679 (p) cc_final: 0.5001 (t) REVERT: B 551 VAL cc_start: 0.8081 (t) cc_final: 0.7530 (p) REVERT: B 563 GLN cc_start: 0.6260 (mt0) cc_final: 0.5182 (mp10) REVERT: B 707 TYR cc_start: 0.6900 (t80) cc_final: 0.6432 (t80) REVERT: B 731 MET cc_start: 0.8200 (ttp) cc_final: 0.7844 (ptm) REVERT: B 759 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6865 (t80) REVERT: B 789 TYR cc_start: 0.8439 (m-80) cc_final: 0.8203 (m-80) REVERT: B 949 GLN cc_start: 0.6673 (tp-100) cc_final: 0.6463 (tp-100) REVERT: B 953 ASN cc_start: 0.8311 (m110) cc_final: 0.7429 (m110) REVERT: B 1001 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7959 (mm) REVERT: D 396 TYR cc_start: 0.6112 (m-80) cc_final: 0.5388 (m-10) REVERT: D 759 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7893 (t80) REVERT: D 902 MET cc_start: 0.8500 (mmm) cc_final: 0.7952 (mmt) REVERT: D 973 ILE cc_start: 0.7410 (tp) cc_final: 0.6952 (mm) REVERT: D 1003 SER cc_start: 0.9196 (p) cc_final: 0.8873 (m) REVERT: D 1028 LYS cc_start: 0.8119 (mttt) cc_final: 0.7672 (mttt) outliers start: 91 outliers final: 48 residues processed: 571 average time/residue: 0.1738 time to fit residues: 165.3365 Evaluate side-chains 463 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 410 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 357 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 chunk 373 optimal weight: 0.9980 chunk 318 optimal weight: 0.5980 chunk 184 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 319 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN C 239 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 388 ASN B 675 GLN B 928 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 641 ASN D 762 GLN D 777 ASN D 901 GLN D1011 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.134461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.115006 restraints weight = 118938.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.116115 restraints weight = 84366.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.116277 restraints weight = 53376.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.116486 restraints weight = 49197.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.116709 restraints weight = 44950.897| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 31748 Z= 0.188 Angle : 0.727 21.446 43327 Z= 0.351 Chirality : 0.049 0.529 5018 Planarity : 0.004 0.056 5481 Dihedral : 6.970 64.662 5584 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.86 % Rotamer: Outliers : 3.10 % Allowed : 12.75 % Favored : 84.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3760 helix: 0.05 (0.16), residues: 1010 sheet: -0.53 (0.17), residues: 696 loop : -1.07 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 115 TYR 0.028 0.002 TYR B 904 PHE 0.018 0.002 PHE D 970 TRP 0.032 0.002 TRP B 886 HIS 0.010 0.002 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00408 (31633) covalent geometry : angle 0.66630 (43027) SS BOND : bond 0.00756 ( 42) SS BOND : angle 2.56435 ( 84) hydrogen bonds : bond 0.04682 ( 1149) hydrogen bonds : angle 6.18570 ( 3228) Misc. bond : bond 0.00050 ( 1) link_BETA1-4 : bond 0.01235 ( 18) link_BETA1-4 : angle 3.98617 ( 54) link_NAG-ASN : bond 0.00960 ( 54) link_NAG-ASN : angle 3.81887 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 447 time to evaluate : 0.773 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 41 TYR cc_start: 0.5674 (t80) cc_final: 0.5102 (t80) REVERT: A 45 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.4789 (mt) REVERT: A 190 MET cc_start: 0.3922 (ptp) cc_final: 0.3618 (ttt) REVERT: A 360 MET cc_start: 0.4722 (ttp) cc_final: 0.4070 (ptm) REVERT: A 428 PHE cc_start: 0.5899 (m-80) cc_final: 0.5321 (m-80) REVERT: A 472 GLN cc_start: 0.6018 (pm20) cc_final: 0.5525 (mt0) REVERT: A 474 MET cc_start: 0.3204 (tpp) cc_final: 0.2898 (tpp) REVERT: A 593 THR cc_start: 0.6569 (m) cc_final: 0.6364 (t) REVERT: C 240 THR cc_start: 0.7528 (m) cc_final: 0.7249 (p) REVERT: C 392 PHE cc_start: 0.7105 (m-80) cc_final: 0.6708 (m-80) REVERT: C 614 ASP cc_start: 0.6234 (t0) cc_final: 0.5738 (t0) REVERT: C 698 SER cc_start: 0.8480 (t) cc_final: 0.7957 (p) REVERT: C 756 TYR cc_start: 0.7586 (m-10) cc_final: 0.7345 (m-10) REVERT: C 775 ASP cc_start: 0.7153 (m-30) cc_final: 0.6896 (m-30) REVERT: C 779 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7169 (tp-100) REVERT: C 864 LEU cc_start: 0.8544 (tp) cc_final: 0.8064 (tt) REVERT: C 901 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8211 (tp40) REVERT: C 959 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8526 (mp) REVERT: C 962 LEU cc_start: 0.9010 (tp) cc_final: 0.8737 (tp) REVERT: B 231 ILE cc_start: 0.6406 (mt) cc_final: 0.6012 (mm) REVERT: B 452 LEU cc_start: 0.7030 (mp) cc_final: 0.6705 (mt) REVERT: B 500 THR cc_start: 0.5651 (p) cc_final: 0.5015 (t) REVERT: B 551 VAL cc_start: 0.8042 (t) cc_final: 0.7485 (p) REVERT: B 731 MET cc_start: 0.8227 (ttp) cc_final: 0.7920 (ptm) REVERT: B 759 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7047 (t80) REVERT: B 789 TYR cc_start: 0.8550 (m-80) cc_final: 0.8196 (m-80) REVERT: B 816 SER cc_start: 0.7992 (p) cc_final: 0.7582 (m) REVERT: B 1001 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7819 (mm) REVERT: D 276 LEU cc_start: 0.7665 (mm) cc_final: 0.7115 (mm) REVERT: D 353 TRP cc_start: 0.7248 (OUTLIER) cc_final: 0.6563 (p-90) REVERT: D 398 ASP cc_start: 0.5493 (m-30) cc_final: 0.4430 (m-30) REVERT: D 902 MET cc_start: 0.8634 (mmm) cc_final: 0.8051 (mmt) REVERT: D 1003 SER cc_start: 0.9273 (p) cc_final: 0.9001 (m) REVERT: D 1102 TRP cc_start: 0.7472 (m100) cc_final: 0.7025 (m100) outliers start: 103 outliers final: 61 residues processed: 518 average time/residue: 0.1720 time to fit residues: 147.9736 Evaluate side-chains 450 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 382 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 353 TRP Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 0.8980 chunk 343 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 176 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 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN B 314 GLN B 755 GLN B 856 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.148412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.124733 restraints weight = 99279.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.125965 restraints weight = 71373.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.126561 restraints weight = 56096.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.126349 restraints weight = 48506.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.126334 restraints weight = 42100.807| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31748 Z= 0.149 Angle : 0.676 21.106 43327 Z= 0.328 Chirality : 0.046 0.363 5018 Planarity : 0.004 0.053 5481 Dihedral : 6.654 59.514 5584 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.48 % Favored : 96.44 % Rotamer: Outliers : 2.68 % Allowed : 14.28 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 3760 helix: 0.26 (0.16), residues: 999 sheet: -0.39 (0.18), residues: 688 loop : -1.02 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 115 TYR 0.022 0.002 TYR B1138 PHE 0.025 0.002 PHE D 329 TRP 0.018 0.001 TRP B 886 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00333 (31633) covalent geometry : angle 0.62997 (43027) SS BOND : bond 0.00379 ( 42) SS BOND : angle 2.38849 ( 84) hydrogen bonds : bond 0.04446 ( 1149) hydrogen bonds : angle 6.06356 ( 3228) Misc. bond : bond 0.00034 ( 1) link_BETA1-4 : bond 0.01113 ( 18) link_BETA1-4 : angle 3.83843 ( 54) link_NAG-ASN : bond 0.00481 ( 54) link_NAG-ASN : angle 3.00514 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 425 time to evaluate : 1.140 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 41 TYR cc_start: 0.5964 (t80) cc_final: 0.5341 (t80) REVERT: A 45 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4826 (mt) REVERT: A 190 MET cc_start: 0.4141 (ptp) cc_final: 0.3700 (ttt) REVERT: A 360 MET cc_start: 0.4381 (ttp) cc_final: 0.3854 (ptm) REVERT: C 495 TYR cc_start: 0.4919 (m-80) cc_final: 0.4576 (m-80) REVERT: C 614 ASP cc_start: 0.6166 (t0) cc_final: 0.5644 (t0) REVERT: C 698 SER cc_start: 0.8427 (t) cc_final: 0.7945 (p) REVERT: C 741 TYR cc_start: 0.8206 (t80) cc_final: 0.7958 (t80) REVERT: C 756 TYR cc_start: 0.7683 (m-10) cc_final: 0.7471 (m-10) REVERT: C 775 ASP cc_start: 0.7018 (m-30) cc_final: 0.6612 (m-30) REVERT: C 780 GLU cc_start: 0.7258 (pt0) cc_final: 0.6539 (pt0) REVERT: C 901 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8194 (tp40) REVERT: C 959 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8487 (mp) REVERT: C 962 LEU cc_start: 0.8937 (tp) cc_final: 0.8319 (tp) REVERT: C 1019 ARG cc_start: 0.7800 (tpt90) cc_final: 0.7287 (tpt170) REVERT: C 1050 MET cc_start: 0.8022 (ptt) cc_final: 0.7740 (ptt) REVERT: B 231 ILE cc_start: 0.6394 (mt) cc_final: 0.6048 (mm) REVERT: B 340 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6893 (mm-30) REVERT: B 500 THR cc_start: 0.6124 (p) cc_final: 0.5463 (t) REVERT: B 551 VAL cc_start: 0.7804 (t) cc_final: 0.7249 (p) REVERT: B 707 TYR cc_start: 0.7173 (t80) cc_final: 0.6091 (m-80) REVERT: B 731 MET cc_start: 0.8133 (ttp) cc_final: 0.7896 (ptm) REVERT: B 737 ASP cc_start: 0.6990 (t0) cc_final: 0.6578 (t0) REVERT: B 759 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7122 (t80) REVERT: B 789 TYR cc_start: 0.8544 (m-80) cc_final: 0.8165 (m-80) REVERT: B 1001 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7710 (mm) REVERT: D 398 ASP cc_start: 0.5254 (m-30) cc_final: 0.5001 (m-30) REVERT: D 902 MET cc_start: 0.8669 (mmm) cc_final: 0.8097 (mmt) REVERT: D 1003 SER cc_start: 0.9175 (p) cc_final: 0.8895 (t) REVERT: D 1102 TRP cc_start: 0.7369 (m100) cc_final: 0.7145 (m100) outliers start: 89 outliers final: 57 residues processed: 484 average time/residue: 0.1761 time to fit residues: 142.0461 Evaluate side-chains 432 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 370 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1101 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 310 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 262 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 755 GLN C 779 GLN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN B 856 ASN D 394 ASN D 777 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.148330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.126093 restraints weight = 100677.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.125920 restraints weight = 84931.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.126064 restraints weight = 69113.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.126010 restraints weight = 66916.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.126081 restraints weight = 63459.557| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31748 Z= 0.142 Angle : 0.649 19.829 43327 Z= 0.317 Chirality : 0.046 0.367 5018 Planarity : 0.004 0.055 5481 Dihedral : 6.510 59.345 5583 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 3.01 % Allowed : 14.40 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 3760 helix: 0.27 (0.16), residues: 1005 sheet: -0.37 (0.18), residues: 692 loop : -1.01 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 115 TYR 0.023 0.002 TYR B1138 PHE 0.026 0.002 PHE C 817 TRP 0.025 0.002 TRP A 163 HIS 0.013 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00316 (31633) covalent geometry : angle 0.60792 (43027) SS BOND : bond 0.00611 ( 42) SS BOND : angle 1.99058 ( 84) hydrogen bonds : bond 0.04193 ( 1149) hydrogen bonds : angle 5.94216 ( 3228) Misc. bond : bond 0.00025 ( 1) link_BETA1-4 : bond 0.01052 ( 18) link_BETA1-4 : angle 3.64665 ( 54) link_NAG-ASN : bond 0.00569 ( 54) link_NAG-ASN : angle 2.84708 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 427 time to evaluate : 1.162 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 45 LEU cc_start: 0.5266 (OUTLIER) cc_final: 0.4698 (mt) REVERT: A 168 TRP cc_start: 0.1219 (t-100) cc_final: -0.0107 (t60) REVERT: A 190 MET cc_start: 0.4249 (ptp) cc_final: 0.3829 (ttt) REVERT: A 360 MET cc_start: 0.4601 (ttp) cc_final: 0.4094 (ptm) REVERT: A 518 ARG cc_start: 0.4857 (ppt170) cc_final: 0.4465 (ppt170) REVERT: C 495 TYR cc_start: 0.4715 (m-80) cc_final: 0.4419 (m-80) REVERT: C 614 ASP cc_start: 0.6148 (t0) cc_final: 0.5642 (t0) REVERT: C 698 SER cc_start: 0.8503 (t) cc_final: 0.8295 (m) REVERT: C 731 MET cc_start: 0.8050 (ptm) cc_final: 0.7781 (ptm) REVERT: C 741 TYR cc_start: 0.8202 (t80) cc_final: 0.7926 (t80) REVERT: C 756 TYR cc_start: 0.7692 (m-10) cc_final: 0.7480 (m-10) REVERT: C 775 ASP cc_start: 0.7086 (m-30) cc_final: 0.6805 (m-30) REVERT: C 780 GLU cc_start: 0.7036 (pt0) cc_final: 0.6522 (pt0) REVERT: C 901 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8272 (tp40) REVERT: C 904 TYR cc_start: 0.6695 (p90) cc_final: 0.6357 (p90) REVERT: C 959 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8544 (mp) REVERT: C 962 LEU cc_start: 0.8938 (tp) cc_final: 0.8352 (tp) REVERT: C 1019 ARG cc_start: 0.7810 (tpt90) cc_final: 0.7589 (tpt170) REVERT: B 231 ILE cc_start: 0.6446 (mt) cc_final: 0.6051 (mm) REVERT: B 298 GLU cc_start: 0.7927 (tp30) cc_final: 0.7618 (tp30) REVERT: B 486 PHE cc_start: 0.4521 (t80) cc_final: 0.4249 (t80) REVERT: B 500 THR cc_start: 0.6060 (p) cc_final: 0.5836 (p) REVERT: B 551 VAL cc_start: 0.7535 (t) cc_final: 0.6999 (p) REVERT: B 731 MET cc_start: 0.8077 (ttp) cc_final: 0.7835 (ptm) REVERT: B 759 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.7137 (t80) REVERT: B 789 TYR cc_start: 0.8573 (m-80) cc_final: 0.8164 (m-80) REVERT: B 869 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7505 (mtp) REVERT: B 949 GLN cc_start: 0.6350 (tp-100) cc_final: 0.5862 (tp-100) REVERT: B 953 ASN cc_start: 0.7804 (m110) cc_final: 0.7093 (m110) REVERT: B 1001 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7571 (mm) REVERT: D 270 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.5076 (mp) REVERT: D 378 LYS cc_start: 0.5575 (OUTLIER) cc_final: 0.5225 (pttm) REVERT: D 396 TYR cc_start: 0.5843 (m-10) cc_final: 0.5527 (m-10) REVERT: D 398 ASP cc_start: 0.5256 (m-30) cc_final: 0.5028 (m-30) REVERT: D 737 ASP cc_start: 0.6012 (p0) cc_final: 0.4782 (p0) REVERT: D 774 GLN cc_start: 0.8569 (mm-40) cc_final: 0.7920 (mm-40) REVERT: D 902 MET cc_start: 0.8668 (mmm) cc_final: 0.8009 (mmt) REVERT: D 1102 TRP cc_start: 0.7370 (m100) cc_final: 0.7164 (m100) outliers start: 100 outliers final: 67 residues processed: 494 average time/residue: 0.1754 time to fit residues: 143.5937 Evaluate side-chains 446 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 371 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1101 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 174 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 354 optimal weight: 0.0670 chunk 105 optimal weight: 0.7980 chunk 324 optimal weight: 0.7980 chunk 249 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN B 751 ASN B 853 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN D 913 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.134521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.114741 restraints weight = 116590.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.116225 restraints weight = 69266.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.117065 restraints weight = 46057.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.117323 restraints weight = 33956.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.117231 restraints weight = 28796.560| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 31748 Z= 0.132 Angle : 0.639 19.236 43327 Z= 0.312 Chirality : 0.045 0.380 5018 Planarity : 0.004 0.050 5481 Dihedral : 6.392 59.940 5583 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.06 % Rotamer: Outliers : 2.68 % Allowed : 14.91 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 3760 helix: 0.32 (0.16), residues: 1009 sheet: -0.33 (0.18), residues: 693 loop : -0.94 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 115 TYR 0.024 0.001 TYR B 369 PHE 0.027 0.002 PHE C 817 TRP 0.061 0.002 TRP A 163 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00292 (31633) covalent geometry : angle 0.59837 (43027) SS BOND : bond 0.00366 ( 42) SS BOND : angle 2.27371 ( 84) hydrogen bonds : bond 0.04136 ( 1149) hydrogen bonds : angle 5.81505 ( 3228) Misc. bond : bond 0.00016 ( 1) link_BETA1-4 : bond 0.01225 ( 18) link_BETA1-4 : angle 3.41281 ( 54) link_NAG-ASN : bond 0.00512 ( 54) link_NAG-ASN : angle 2.71639 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 427 time to evaluate : 1.119 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 45 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.4918 (mt) REVERT: A 168 TRP cc_start: 0.1293 (t-100) cc_final: -0.0039 (t60) REVERT: A 190 MET cc_start: 0.4261 (ptp) cc_final: 0.3858 (ttt) REVERT: A 327 PHE cc_start: 0.4736 (t80) cc_final: 0.3869 (t80) REVERT: A 360 MET cc_start: 0.4529 (ttp) cc_final: 0.4096 (mtp) REVERT: A 474 MET cc_start: 0.3201 (tpp) cc_final: 0.2416 (mmt) REVERT: A 518 ARG cc_start: 0.4655 (ppt170) cc_final: 0.3868 (ppt170) REVERT: A 592 PHE cc_start: 0.3950 (t80) cc_final: 0.3734 (t80) REVERT: C 495 TYR cc_start: 0.4675 (m-80) cc_final: 0.4374 (m-80) REVERT: C 614 ASP cc_start: 0.6021 (t0) cc_final: 0.5489 (t0) REVERT: C 698 SER cc_start: 0.8614 (t) cc_final: 0.8310 (m) REVERT: C 756 TYR cc_start: 0.7800 (m-10) cc_final: 0.7497 (m-10) REVERT: C 775 ASP cc_start: 0.7145 (m-30) cc_final: 0.6705 (m-30) REVERT: C 780 GLU cc_start: 0.7325 (pt0) cc_final: 0.6884 (pt0) REVERT: C 901 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8286 (tp40) REVERT: C 959 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8592 (mp) REVERT: C 962 LEU cc_start: 0.8928 (tp) cc_final: 0.8570 (tp) REVERT: C 1019 ARG cc_start: 0.7842 (tpt90) cc_final: 0.7569 (tpt170) REVERT: B 231 ILE cc_start: 0.6015 (mt) cc_final: 0.5605 (mm) REVERT: B 298 GLU cc_start: 0.7809 (tp30) cc_final: 0.7602 (tp30) REVERT: B 387 LEU cc_start: 0.5899 (mt) cc_final: 0.5694 (tp) REVERT: B 486 PHE cc_start: 0.4681 (t80) cc_final: 0.4439 (t80) REVERT: B 500 THR cc_start: 0.5967 (p) cc_final: 0.5709 (p) REVERT: B 551 VAL cc_start: 0.8051 (t) cc_final: 0.7468 (p) REVERT: B 707 TYR cc_start: 0.7084 (t80) cc_final: 0.6005 (m-80) REVERT: B 731 MET cc_start: 0.8045 (ttp) cc_final: 0.7792 (ptm) REVERT: B 737 ASP cc_start: 0.6667 (t0) cc_final: 0.6361 (t0) REVERT: B 759 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7212 (t80) REVERT: B 789 TYR cc_start: 0.8473 (m-80) cc_final: 0.8132 (m-80) REVERT: B 855 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: B 1001 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7691 (mm) REVERT: B 1019 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7325 (tpt90) REVERT: B 1063 LEU cc_start: 0.8168 (mt) cc_final: 0.7951 (mt) REVERT: D 396 TYR cc_start: 0.5717 (m-10) cc_final: 0.5470 (m-10) REVERT: D 398 ASP cc_start: 0.5857 (m-30) cc_final: 0.5506 (m-30) REVERT: D 774 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7637 (mm-40) REVERT: D 902 MET cc_start: 0.8609 (mmm) cc_final: 0.7998 (mmt) REVERT: D 950 ASP cc_start: 0.7263 (m-30) cc_final: 0.6950 (m-30) outliers start: 89 outliers final: 63 residues processed: 482 average time/residue: 0.1750 time to fit residues: 140.0928 Evaluate side-chains 458 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 389 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 103 optimal weight: 10.0000 chunk 135 optimal weight: 0.0070 chunk 371 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 197 optimal weight: 0.0870 chunk 235 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 269 optimal weight: 6.9990 chunk 107 optimal weight: 0.0270 chunk 51 optimal weight: 0.4980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN D1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.148270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.124919 restraints weight = 101386.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.126048 restraints weight = 73174.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.126673 restraints weight = 57108.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.126192 restraints weight = 49606.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.126099 restraints weight = 42792.913| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 31748 Z= 0.127 Angle : 0.637 18.728 43327 Z= 0.314 Chirality : 0.045 0.363 5018 Planarity : 0.004 0.048 5481 Dihedral : 6.296 59.421 5583 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 2.68 % Allowed : 15.63 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 3760 helix: 0.37 (0.16), residues: 1016 sheet: -0.24 (0.18), residues: 665 loop : -0.93 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 102 TYR 0.026 0.002 TYR B 369 PHE 0.032 0.001 PHE A 230 TRP 0.059 0.002 TRP A 163 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00282 (31633) covalent geometry : angle 0.60190 (43027) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.94176 ( 84) hydrogen bonds : bond 0.04052 ( 1149) hydrogen bonds : angle 5.73086 ( 3228) Misc. bond : bond 0.00018 ( 1) link_BETA1-4 : bond 0.01045 ( 18) link_BETA1-4 : angle 3.20840 ( 54) link_NAG-ASN : bond 0.00469 ( 54) link_NAG-ASN : angle 2.64183 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 418 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5053 (mt) REVERT: A 144 LEU cc_start: 0.3759 (tp) cc_final: 0.3356 (tp) REVERT: A 168 TRP cc_start: 0.1454 (t-100) cc_final: 0.0168 (t60) REVERT: A 190 MET cc_start: 0.4370 (ptp) cc_final: 0.3881 (ttt) REVERT: A 327 PHE cc_start: 0.5053 (t80) cc_final: 0.4308 (t80) REVERT: A 360 MET cc_start: 0.4051 (ttp) cc_final: 0.3481 (mtm) REVERT: C 495 TYR cc_start: 0.4829 (m-80) cc_final: 0.4434 (m-80) REVERT: C 614 ASP cc_start: 0.5958 (t0) cc_final: 0.5419 (t0) REVERT: C 698 SER cc_start: 0.8531 (t) cc_final: 0.7962 (p) REVERT: C 775 ASP cc_start: 0.7097 (m-30) cc_final: 0.6657 (m-30) REVERT: C 780 GLU cc_start: 0.7251 (pt0) cc_final: 0.6849 (pt0) REVERT: C 901 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8069 (tp40) REVERT: C 959 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8728 (mp) REVERT: B 387 LEU cc_start: 0.5899 (mt) cc_final: 0.5688 (tp) REVERT: B 486 PHE cc_start: 0.4609 (t80) cc_final: 0.4362 (t80) REVERT: B 500 THR cc_start: 0.6112 (p) cc_final: 0.5878 (p) REVERT: B 551 VAL cc_start: 0.7801 (t) cc_final: 0.7219 (p) REVERT: B 707 TYR cc_start: 0.7055 (t80) cc_final: 0.5902 (m-80) REVERT: B 731 MET cc_start: 0.7986 (ttp) cc_final: 0.7772 (ptm) REVERT: B 759 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7279 (t80) REVERT: B 789 TYR cc_start: 0.8549 (m-80) cc_final: 0.8205 (m-80) REVERT: B 855 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.5769 (m-80) REVERT: B 954 GLN cc_start: 0.7490 (mt0) cc_final: 0.7230 (mt0) REVERT: B 1019 ARG cc_start: 0.7832 (tpp-160) cc_final: 0.7055 (tpt90) REVERT: B 1063 LEU cc_start: 0.8246 (mt) cc_final: 0.7945 (mt) REVERT: D 195 LYS cc_start: 0.6727 (tmmt) cc_final: 0.6482 (tptp) REVERT: D 365 TYR cc_start: 0.4686 (m-10) cc_final: 0.3990 (m-10) REVERT: D 774 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7948 (mm-40) REVERT: D 902 MET cc_start: 0.8602 (mmm) cc_final: 0.8044 (mmt) REVERT: D 950 ASP cc_start: 0.7331 (m-30) cc_final: 0.7115 (m-30) outliers start: 89 outliers final: 63 residues processed: 474 average time/residue: 0.1718 time to fit residues: 136.0833 Evaluate side-chains 447 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 379 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 991 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 317 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 320 optimal weight: 0.0070 chunk 194 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN C 245 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 955 ASN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.147527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.125102 restraints weight = 101835.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.125172 restraints weight = 80817.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.124855 restraints weight = 73606.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.125092 restraints weight = 68085.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.125079 restraints weight = 60372.876| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 31748 Z= 0.134 Angle : 0.636 18.198 43327 Z= 0.315 Chirality : 0.045 0.374 5018 Planarity : 0.004 0.049 5481 Dihedral : 6.233 59.057 5583 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 2.41 % Allowed : 16.39 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 3760 helix: 0.44 (0.16), residues: 1017 sheet: -0.31 (0.18), residues: 677 loop : -0.95 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 115 TYR 0.024 0.002 TYR A 199 PHE 0.021 0.002 PHE C 32 TRP 0.055 0.002 TRP A 163 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (31633) covalent geometry : angle 0.60287 (43027) SS BOND : bond 0.00342 ( 42) SS BOND : angle 1.84657 ( 84) hydrogen bonds : bond 0.03999 ( 1149) hydrogen bonds : angle 5.71543 ( 3228) Misc. bond : bond 0.00027 ( 1) link_BETA1-4 : bond 0.01078 ( 18) link_BETA1-4 : angle 3.08497 ( 54) link_NAG-ASN : bond 0.00444 ( 54) link_NAG-ASN : angle 2.58909 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 412 time to evaluate : 1.253 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 45 LEU cc_start: 0.5558 (OUTLIER) cc_final: 0.4990 (mt) REVERT: A 190 MET cc_start: 0.4365 (ptp) cc_final: 0.3841 (ttt) REVERT: A 327 PHE cc_start: 0.4971 (t80) cc_final: 0.4344 (t80) REVERT: A 341 LYS cc_start: 0.4494 (mtmm) cc_final: 0.3920 (pptt) REVERT: A 360 MET cc_start: 0.4122 (ttp) cc_final: 0.3734 (mtm) REVERT: A 474 MET cc_start: 0.3233 (tpp) cc_final: 0.2293 (mmt) REVERT: C 495 TYR cc_start: 0.4802 (m-80) cc_final: 0.4450 (m-80) REVERT: C 614 ASP cc_start: 0.6128 (t0) cc_final: 0.5578 (t0) REVERT: C 775 ASP cc_start: 0.7028 (m-30) cc_final: 0.6626 (m-30) REVERT: C 901 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8109 (tp40) REVERT: C 959 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8721 (mp) REVERT: C 962 LEU cc_start: 0.9066 (tp) cc_final: 0.8584 (tp) REVERT: B 486 PHE cc_start: 0.4537 (t80) cc_final: 0.4270 (t80) REVERT: B 500 THR cc_start: 0.6192 (p) cc_final: 0.5948 (p) REVERT: B 551 VAL cc_start: 0.7445 (t) cc_final: 0.6907 (p) REVERT: B 759 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7186 (t80) REVERT: B 855 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: B 954 GLN cc_start: 0.7472 (mt0) cc_final: 0.7235 (mt0) REVERT: B 1019 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7107 (tpt90) REVERT: B 1063 LEU cc_start: 0.8178 (mt) cc_final: 0.7809 (mt) REVERT: B 1065 VAL cc_start: 0.9152 (t) cc_final: 0.8946 (p) REVERT: D 195 LYS cc_start: 0.7499 (tmmt) cc_final: 0.7205 (tptp) REVERT: D 473 TYR cc_start: 0.4550 (t80) cc_final: 0.4093 (t80) REVERT: D 731 MET cc_start: 0.8672 (ptm) cc_final: 0.8312 (ptm) REVERT: D 902 MET cc_start: 0.8656 (mmm) cc_final: 0.8052 (mmt) REVERT: D 950 ASP cc_start: 0.7372 (m-30) cc_final: 0.7132 (m-30) outliers start: 80 outliers final: 59 residues processed: 462 average time/residue: 0.1744 time to fit residues: 134.3855 Evaluate side-chains 440 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 376 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 939 SER Chi-restraints excluded: chain D residue 991 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1101 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 78 optimal weight: 0.0670 chunk 223 optimal weight: 0.8980 chunk 335 optimal weight: 6.9990 chunk 31 optimal weight: 0.0060 chunk 222 optimal weight: 3.9990 chunk 91 optimal weight: 0.0030 chunk 225 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 168 optimal weight: 0.0470 chunk 35 optimal weight: 4.9990 overall best weight: 0.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 501 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.148379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.125546 restraints weight = 101978.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.126174 restraints weight = 76728.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.125903 restraints weight = 61955.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.126505 restraints weight = 58391.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.126074 restraints weight = 55182.113| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 31748 Z= 0.120 Angle : 0.634 17.977 43327 Z= 0.313 Chirality : 0.045 0.362 5018 Planarity : 0.004 0.062 5481 Dihedral : 6.068 57.004 5583 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.51 % Favored : 96.38 % Rotamer: Outliers : 1.59 % Allowed : 17.53 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 3760 helix: 0.42 (0.16), residues: 1024 sheet: -0.12 (0.19), residues: 625 loop : -0.92 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 815 TYR 0.020 0.001 TYR B1138 PHE 0.028 0.001 PHE C 135 TRP 0.055 0.002 TRP A 163 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00264 (31633) covalent geometry : angle 0.60330 (43027) SS BOND : bond 0.00353 ( 42) SS BOND : angle 1.72928 ( 84) hydrogen bonds : bond 0.03909 ( 1149) hydrogen bonds : angle 5.59519 ( 3228) Misc. bond : bond 0.00014 ( 1) link_BETA1-4 : bond 0.01041 ( 18) link_BETA1-4 : angle 3.03547 ( 54) link_NAG-ASN : bond 0.00432 ( 54) link_NAG-ASN : angle 2.51475 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 424 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.4985 (mt) REVERT: A 168 TRP cc_start: 0.1114 (t-100) cc_final: -0.0394 (t60) REVERT: A 190 MET cc_start: 0.4581 (ptp) cc_final: 0.3953 (ttt) REVERT: A 327 PHE cc_start: 0.4923 (t80) cc_final: 0.4248 (t80) REVERT: A 341 LYS cc_start: 0.5003 (mtmm) cc_final: 0.4417 (pptt) REVERT: A 360 MET cc_start: 0.4007 (ttp) cc_final: 0.3674 (mtm) REVERT: A 474 MET cc_start: 0.3371 (tpp) cc_final: 0.2554 (mmt) REVERT: A 564 GLU cc_start: 0.6541 (tp30) cc_final: 0.5009 (mp0) REVERT: C 217 PRO cc_start: 0.3757 (Cg_endo) cc_final: 0.3119 (Cg_exo) REVERT: C 495 TYR cc_start: 0.4980 (m-80) cc_final: 0.4662 (m-80) REVERT: C 614 ASP cc_start: 0.6126 (t0) cc_final: 0.5623 (t0) REVERT: C 775 ASP cc_start: 0.7000 (m-30) cc_final: 0.6649 (m-30) REVERT: C 901 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7994 (tp40) REVERT: C 931 ILE cc_start: 0.8400 (mm) cc_final: 0.8047 (mm) REVERT: C 959 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8722 (mp) REVERT: B 309 GLU cc_start: 0.7216 (tm-30) cc_final: 0.6832 (tm-30) REVERT: B 486 PHE cc_start: 0.4660 (t80) cc_final: 0.4446 (t80) REVERT: B 500 THR cc_start: 0.6289 (p) cc_final: 0.6049 (p) REVERT: B 551 VAL cc_start: 0.7484 (t) cc_final: 0.6970 (p) REVERT: B 707 TYR cc_start: 0.7083 (t80) cc_final: 0.5926 (m-80) REVERT: B 820 ASP cc_start: 0.6424 (m-30) cc_final: 0.5992 (m-30) REVERT: B 855 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: B 954 GLN cc_start: 0.7577 (mt0) cc_final: 0.7348 (mt0) REVERT: B 1019 ARG cc_start: 0.7956 (tpp-160) cc_final: 0.7286 (tpt90) REVERT: B 1063 LEU cc_start: 0.8080 (mt) cc_final: 0.7808 (mt) REVERT: D 54 LEU cc_start: 0.6309 (mm) cc_final: 0.6014 (tp) REVERT: D 195 LYS cc_start: 0.7584 (tmmt) cc_final: 0.7277 (tptp) REVERT: D 302 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7616 (p) REVERT: D 355 ARG cc_start: 0.4756 (ttt180) cc_final: 0.4345 (mtp180) REVERT: D 473 TYR cc_start: 0.4642 (t80) cc_final: 0.4205 (t80) REVERT: D 902 MET cc_start: 0.8588 (mmm) cc_final: 0.8002 (mmt) outliers start: 53 outliers final: 41 residues processed: 455 average time/residue: 0.1755 time to fit residues: 133.2441 Evaluate side-chains 429 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 383 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 275 TRP Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 331 optimal weight: 0.8980 chunk 315 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 347 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.145929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.123417 restraints weight = 103277.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.123701 restraints weight = 81087.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.123332 restraints weight = 74515.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.123898 restraints weight = 62942.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.123846 restraints weight = 52908.664| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 31748 Z= 0.156 Angle : 0.659 17.227 43327 Z= 0.327 Chirality : 0.045 0.378 5018 Planarity : 0.004 0.085 5481 Dihedral : 6.266 59.610 5583 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 1.86 % Allowed : 17.35 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 3760 helix: 0.46 (0.16), residues: 1024 sheet: -0.18 (0.19), residues: 613 loop : -0.93 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 214 TYR 0.030 0.002 TYR C 904 PHE 0.017 0.002 PHE C 32 TRP 0.056 0.002 TRP A 163 HIS 0.008 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00352 (31633) covalent geometry : angle 0.62785 (43027) SS BOND : bond 0.00339 ( 42) SS BOND : angle 1.90442 ( 84) hydrogen bonds : bond 0.03978 ( 1149) hydrogen bonds : angle 5.66155 ( 3228) Misc. bond : bond 0.00015 ( 1) link_BETA1-4 : bond 0.01069 ( 18) link_BETA1-4 : angle 3.09794 ( 54) link_NAG-ASN : bond 0.00440 ( 54) link_NAG-ASN : angle 2.52818 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5838.31 seconds wall clock time: 101 minutes 35.54 seconds (6095.54 seconds total)