Starting phenix.real_space_refine on Sun Jul 5 23:45:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7df4_30661/07_2026/7df4_30661.cif Found real_map, /net/cci-nas-00/data/ceres_data/7df4_30661/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7df4_30661/07_2026/7df4_30661.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7df4_30661/07_2026/7df4_30661.cif" model { file = "/net/cci-nas-00/data/ceres_data/7df4_30661/07_2026/7df4_30661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7df4_30661/07_2026/7df4_30661.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7df4_30661/07_2026/7df4_30661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7df4_30661/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 13 Time building chain proxies: 5.89, per 1000 atoms: 0.19 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: 2.50 Conformation dependent library (CDL) restraints added in 995.2 milliseconds 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: 1.34 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: 6.60 Time building geometry restraints manager: 3.20 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: 17764 15.84 - 31.69: 358 31.69 - 47.53: 95 47.53 - 63.37: 25 63.37 - 79.22: 2 Dihedral angle restraints: 18244 sinusoidal: 7169 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 18241 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: 4.560 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.490 Find NCS groups from input model: 0.710 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 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 : 7.567 79.218 10988 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/Z covalent geometry : bond 0.00352 / 0.18 (31633) covalent geometry : angle 0.57204 / 0.29 (43027) SS BOND : bond 0.00164 / 0.10 ( 42) SS BOND : angle 0.89851 / 0.60 ( 84) hydrogen bonds : bond 0.28624 / 18.79 ( 1149) hydrogen bonds : angle 10.19141 / 7.19 ( 3228) Misc. bond : bond 0.23728 / 12.49 ( 1) link_BETA1-4 : bond 0.00706 / 0.39 ( 18) link_BETA1-4 : angle 3.62924 / 2.52 ( 54) link_NAG-ASN : bond 0.01227 / 0.95 ( 54) link_NAG-ASN : angle 4.28814 / 3.10 ( 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 : 0.918 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: 0.1874 time to fit residues: 314.5174 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 : 1.029 ------------------------------------------------------------------------------- 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... 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 546 ASN 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: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.136106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.115220 restraints weight = 119305.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.116621 restraints weight = 67114.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.117450 restraints weight = 43561.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.117996 restraints weight = 32178.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.118265 restraints weight = 26267.577| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31748 Z= 0.246 Angle : 0.840 18.252 43327 Z= 0.407 Chirality : 0.052 0.411 5018 Planarity : 0.005 0.053 5481 Dihedral : 4.711 30.230 4076 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 3.43 % Allowed : 9.17 % Favored : 87.40 % 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: -1.45 (0.12), residues: 3760 helix: -0.83 (0.14), residues: 1007 sheet: -0.75 (0.17), residues: 690 loop : -1.05 (0.12), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 115 TYR 0.025 0.003 TYR D 269 PHE 0.032 0.003 PHE B 201 TRP 0.037 0.003 TRP C 64 HIS 0.007 0.002 HIS D1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 (31633) covalent geometry : angle 0.79375 / 0.40 (43027) SS BOND : bond 0.01188 / 0.73 ( 42) SS BOND : angle 2.86968 / 2.38 ( 84) hydrogen bonds : bond 0.06023 / 4.03 ( 1149) hydrogen bonds : angle 6.93266 / 4.90 ( 3228) Misc. bond : bond 0.01242 / 0.65 ( 1) link_BETA1-4 : bond 0.01904 / 0.99 ( 18) link_BETA1-4 : angle 4.06004 / 2.95 ( 54) link_NAG-ASN : bond 0.00778 / 0.56 ( 54) link_NAG-ASN : angle 3.40721 / 2.54 ( 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 679 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 565 time to evaluate : 1.252 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: A 41 TYR cc_start: 0.5938 (t80) cc_final: 0.5232 (t80) REVERT: A 45 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.4861 (mt) REVERT: A 145 GLU cc_start: 0.4626 (mt-10) cc_final: 0.4271 (pp20) REVERT: A 168 TRP cc_start: 0.1296 (t-100) cc_final: 0.0191 (t60) REVERT: A 360 MET cc_start: 0.4579 (ttp) cc_final: 0.3813 (ptm) REVERT: A 428 PHE cc_start: 0.5576 (m-80) cc_final: 0.5237 (m-80) REVERT: A 474 MET cc_start: 0.3739 (tpp) cc_final: 0.3515 (tpp) REVERT: A 592 PHE cc_start: 0.3529 (t80) cc_final: 0.3240 (t80) REVERT: C 240 THR cc_start: 0.7425 (m) cc_final: 0.7209 (p) REVERT: C 270 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.6595 (tp) REVERT: C 310 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8823 (tttp) REVERT: C 380 TYR cc_start: 0.5809 (m-80) cc_final: 0.5040 (m-10) REVERT: C 614 ASP cc_start: 0.6371 (t0) cc_final: 0.6013 (t0) REVERT: C 698 SER cc_start: 0.8489 (t) cc_final: 0.7971 (p) REVERT: C 756 TYR cc_start: 0.7559 (m-10) cc_final: 0.7283 (m-10) REVERT: C 774 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8323 (mm110) REVERT: C 775 ASP cc_start: 0.7062 (m-30) cc_final: 0.6680 (m-30) REVERT: C 780 GLU cc_start: 0.7456 (pt0) cc_final: 0.6652 (pt0) REVERT: C 878 LEU cc_start: 0.9035 (mt) cc_final: 0.8659 (mt) REVERT: C 965 GLN cc_start: 0.7855 (mm110) cc_final: 0.7503 (mt0) REVERT: C 993 ILE cc_start: 0.8560 (pt) cc_final: 0.8273 (pt) REVERT: B 106 PHE cc_start: 0.5718 (m-10) cc_final: 0.5445 (m-80) REVERT: B 451 TYR cc_start: 0.4476 (m-10) cc_final: 0.4169 (m-80) REVERT: B 452 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6748 (mt) REVERT: B 500 THR cc_start: 0.5875 (p) cc_final: 0.5372 (t) REVERT: B 707 TYR cc_start: 0.7208 (t80) cc_final: 0.6907 (t80) REVERT: B 731 MET cc_start: 0.8540 (ttp) cc_final: 0.8121 (ptm) REVERT: B 789 TYR cc_start: 0.8609 (m-80) cc_final: 0.8306 (m-80) REVERT: B 931 ILE cc_start: 0.8838 (mm) cc_final: 0.8605 (mt) REVERT: B 950 ASP cc_start: 0.6488 (m-30) cc_final: 0.6263 (m-30) REVERT: B 1029 MET cc_start: 0.8402 (tpp) cc_final: 0.8195 (tpp) REVERT: D 304 LYS cc_start: 0.8098 (mttt) cc_final: 0.7458 (tttt) REVERT: D 321 GLN cc_start: 0.6731 (OUTLIER) cc_final: 0.4723 (pt0) REVERT: D 353 TRP cc_start: 0.6881 (OUTLIER) cc_final: 0.6585 (p-90) REVERT: D 394 ASN cc_start: 0.4918 (OUTLIER) cc_final: 0.4265 (t160) REVERT: D 396 TYR cc_start: 0.5787 (m-80) cc_final: 0.4787 (m-10) REVERT: D 902 MET cc_start: 0.8527 (mmm) cc_final: 0.8099 (mmt) REVERT: D 973 ILE cc_start: 0.7749 (tp) cc_final: 0.7488 (mm) REVERT: D 1003 SER cc_start: 0.9267 (p) cc_final: 0.9036 (m) REVERT: D 1028 LYS cc_start: 0.8169 (mttt) cc_final: 0.7844 (mttt) REVERT: D 1030 SER cc_start: 0.9099 (m) cc_final: 0.8739 (m) outliers start: 114 outliers final: 67 residues processed: 638 average time/residue: 0.1854 time to fit residues: 193.9829 Evaluate side-chains 504 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 430 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 310 LYS 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 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 154 GLU 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 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 271 GLN 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: 4.9990 chunk 319 optimal weight: 5.9990 chunk 65 optimal weight: 0.1980 chunk 343 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 324 optimal weight: 0.9990 chunk 347 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 388 ASN B 658 ASN B 856 ASN B 901 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN 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 965 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.136262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.116917 restraints weight = 117885.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.118152 restraints weight = 77110.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.118325 restraints weight = 49000.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.118477 restraints weight = 49103.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.118529 restraints weight = 45113.005| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31748 Z= 0.149 Angle : 0.715 20.139 43327 Z= 0.346 Chirality : 0.047 0.492 5018 Planarity : 0.004 0.065 5481 Dihedral : 4.560 27.464 4072 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 2.92 % Allowed : 11.46 % Favored : 85.63 % 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: -1.08 (0.12), residues: 3760 helix: -0.18 (0.15), residues: 1019 sheet: -0.58 (0.17), residues: 695 loop : -0.99 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 115 TYR 0.027 0.002 TYR B 904 PHE 0.026 0.002 PHE D 347 TRP 0.028 0.002 TRP B 886 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (31633) covalent geometry : angle 0.67042 / 0.33 (43027) SS BOND : bond 0.00230 / 0.16 ( 42) SS BOND : angle 3.09265 / 2.37 ( 84) hydrogen bonds : bond 0.05121 / 3.40 ( 1149) hydrogen bonds : angle 6.41230 / 4.51 ( 3228) Misc. bond : bond 0.00166 / 0.09 ( 1) link_BETA1-4 : bond 0.01332 / 0.68 ( 18) link_BETA1-4 : angle 3.79580 / 2.77 ( 54) link_NAG-ASN : bond 0.00483 / 0.32 ( 54) link_NAG-ASN : angle 2.72921 / 1.94 ( 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 596 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 499 time to evaluate : 0.866 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: 0.5760 (t80) cc_final: 0.5059 (t80) REVERT: A 45 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.4786 (mt) REVERT: A 145 GLU cc_start: 0.4652 (mt-10) cc_final: 0.4179 (pp20) REVERT: A 168 TRP cc_start: 0.1303 (t-100) cc_final: 0.0131 (t60) REVERT: A 270 MET cc_start: 0.1137 (mtm) cc_final: 0.0849 (mtm) REVERT: A 360 MET cc_start: 0.4686 (ttp) cc_final: 0.3988 (ptm) REVERT: A 391 LEU cc_start: 0.4398 (mt) cc_final: 0.4181 (mt) REVERT: A 428 PHE cc_start: 0.5705 (m-80) cc_final: 0.5364 (m-80) REVERT: A 462 MET cc_start: 0.3403 (mtt) cc_final: 0.3124 (mtt) REVERT: A 593 THR cc_start: 0.6705 (m) cc_final: 0.6390 (t) REVERT: C 240 THR cc_start: 0.7557 (m) cc_final: 0.7344 (p) REVERT: C 614 ASP cc_start: 0.6238 (t0) cc_final: 0.5751 (t0) REVERT: C 698 SER cc_start: 0.8496 (t) cc_final: 0.8007 (p) REVERT: C 756 TYR cc_start: 0.7452 (m-10) cc_final: 0.7141 (m-10) REVERT: C 775 ASP cc_start: 0.7086 (m-30) cc_final: 0.6684 (m-30) REVERT: C 780 GLU cc_start: 0.7429 (pt0) cc_final: 0.7099 (pt0) REVERT: C 865 LEU cc_start: 0.8737 (mp) cc_final: 0.8233 (mp) REVERT: C 959 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8337 (mp) REVERT: C 962 LEU cc_start: 0.8880 (tp) cc_final: 0.8456 (tp) REVERT: C 965 GLN cc_start: 0.7734 (mm110) cc_final: 0.7271 (mm-40) REVERT: B 452 LEU cc_start: 0.7050 (mp) cc_final: 0.6651 (mt) REVERT: B 500 THR cc_start: 0.5846 (p) cc_final: 0.5161 (t) REVERT: B 551 VAL cc_start: 0.8025 (t) cc_final: 0.7516 (p) REVERT: B 707 TYR cc_start: 0.7013 (t80) cc_final: 0.6577 (t80) REVERT: B 731 MET cc_start: 0.8256 (ttp) cc_final: 0.7901 (ptm) REVERT: B 759 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7329 (t80) REVERT: B 789 TYR cc_start: 0.8515 (m-80) cc_final: 0.8241 (m-80) REVERT: B 949 GLN cc_start: 0.6728 (tp-100) cc_final: 0.6458 (tp-100) REVERT: B 953 ASN cc_start: 0.8358 (m110) cc_final: 0.7445 (m110) REVERT: B 1029 MET cc_start: 0.8418 (tpp) cc_final: 0.8189 (tpp) REVERT: D 275 PHE cc_start: 0.6781 (m-10) cc_final: 0.6576 (m-80) REVERT: D 396 TYR cc_start: 0.5966 (m-80) cc_final: 0.5309 (m-10) REVERT: D 398 ASP cc_start: 0.5696 (m-30) cc_final: 0.5492 (m-30) REVERT: D 902 MET cc_start: 0.8560 (mmm) cc_final: 0.8027 (mmt) REVERT: D 973 ILE cc_start: 0.7457 (tp) cc_final: 0.6992 (mm) REVERT: D 1003 SER cc_start: 0.9251 (p) cc_final: 0.8975 (m) REVERT: D 1028 LYS cc_start: 0.8149 (mttt) cc_final: 0.7705 (mttt) REVERT: D 1030 SER cc_start: 0.8793 (m) cc_final: 0.8592 (m) outliers start: 97 outliers final: 58 residues processed: 561 average time/residue: 0.1707 time to fit residues: 159.8151 Evaluate side-chains 475 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 414 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain C residue 42 VAL 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 284 THR 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 739 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 805 ILE 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 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 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 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE 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 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 301 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 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: 0.7980 chunk 11 optimal weight: 0.8980 chunk 297 optimal weight: 0.9990 chunk 373 optimal weight: 0.9990 chunk 318 optimal weight: 0.0770 chunk 184 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 319 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 409 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN B 314 GLN B 658 ASN B 675 GLN B 856 ASN D 641 ASN D 777 ASN D 901 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.135878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.115844 restraints weight = 117405.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.117500 restraints weight = 74651.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.117961 restraints weight = 44523.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.118008 restraints weight = 36778.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.118140 restraints weight = 37685.236| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 31748 Z= 0.145 Angle : 0.682 17.722 43327 Z= 0.330 Chirality : 0.047 0.644 5018 Planarity : 0.004 0.054 5481 Dihedral : 4.537 26.072 4072 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.81 % Rotamer: Outliers : 2.95 % Allowed : 12.54 % Favored : 84.52 % 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: -0.91 (0.13), residues: 3760 helix: 0.11 (0.16), residues: 1004 sheet: -0.51 (0.17), residues: 683 loop : -0.96 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 115 TYR 0.028 0.002 TYR B 904 PHE 0.019 0.002 PHE D 201 TRP 0.035 0.002 TRP A 566 HIS 0.006 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (31633) covalent geometry : angle 0.64016 / 0.32 (43027) SS BOND : bond 0.00336 / 0.22 ( 42) SS BOND : angle 2.60081 / 1.77 ( 84) hydrogen bonds : bond 0.04587 / 3.05 ( 1149) hydrogen bonds : angle 6.10576 / 4.28 ( 3228) Misc. bond : bond 0.00019 / 0.01 ( 1) link_BETA1-4 : bond 0.01205 / 0.63 ( 18) link_BETA1-4 : angle 3.80283 / 2.77 ( 54) link_NAG-ASN : bond 0.00660 / 0.37 ( 54) link_NAG-ASN : angle 2.66724 / 1.87 ( 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 558 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 460 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.5800 (t80) cc_final: 0.5085 (t80) REVERT: A 45 LEU cc_start: 0.5349 (OUTLIER) cc_final: 0.4742 (mt) REVERT: A 190 MET cc_start: 0.3805 (ptp) cc_final: 0.3521 (ttp) REVERT: A 360 MET cc_start: 0.4620 (ttp) cc_final: 0.3985 (ptm) REVERT: A 428 PHE cc_start: 0.5943 (m-80) cc_final: 0.5446 (m-80) REVERT: A 472 GLN cc_start: 0.6274 (pt0) cc_final: 0.5737 (mm-40) REVERT: A 518 ARG cc_start: 0.4982 (ppt170) cc_final: 0.4510 (ppt170) REVERT: C 240 THR cc_start: 0.7610 (m) cc_final: 0.7362 (p) REVERT: C 434 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6425 (mt) REVERT: C 614 ASP cc_start: 0.6219 (t0) cc_final: 0.5698 (t0) REVERT: C 698 SER cc_start: 0.8445 (t) cc_final: 0.7946 (p) REVERT: C 741 TYR cc_start: 0.8298 (t80) cc_final: 0.8049 (t80) REVERT: C 756 TYR cc_start: 0.7505 (m-10) cc_final: 0.7281 (m-10) REVERT: C 779 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7115 (tp-100) REVERT: C 901 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8281 (tp40) REVERT: C 959 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8399 (mp) REVERT: C 962 LEU cc_start: 0.8901 (tp) cc_final: 0.8388 (tp) REVERT: C 965 GLN cc_start: 0.7794 (mm110) cc_final: 0.7459 (mm-40) REVERT: C 1019 ARG cc_start: 0.7630 (tpt90) cc_final: 0.7299 (tpt170) REVERT: C 1029 MET cc_start: 0.8263 (tpp) cc_final: 0.7961 (tpt) REVERT: B 231 ILE cc_start: 0.6307 (mt) cc_final: 0.5895 (mm) REVERT: B 500 THR cc_start: 0.5917 (p) cc_final: 0.5252 (t) REVERT: B 551 VAL cc_start: 0.7997 (t) cc_final: 0.7444 (p) REVERT: B 707 TYR cc_start: 0.7051 (t80) cc_final: 0.6590 (t80) REVERT: B 731 MET cc_start: 0.8202 (ttp) cc_final: 0.7867 (ptm) REVERT: B 789 TYR cc_start: 0.8507 (m-80) cc_final: 0.8167 (m-80) REVERT: B 949 GLN cc_start: 0.6455 (tp-100) cc_final: 0.6176 (tp-100) REVERT: B 953 ASN cc_start: 0.8365 (m110) cc_final: 0.7770 (m110) REVERT: B 1029 MET cc_start: 0.8173 (tpp) cc_final: 0.7945 (tpp) REVERT: D 398 ASP cc_start: 0.5858 (m-30) cc_final: 0.5573 (m-30) REVERT: D 902 MET cc_start: 0.8584 (mmm) cc_final: 0.8006 (mmt) REVERT: D 1003 SER cc_start: 0.9219 (p) cc_final: 0.8987 (m) REVERT: D 1102 TRP cc_start: 0.7363 (m100) cc_final: 0.6860 (m100) outliers start: 98 outliers final: 58 residues processed: 524 average time/residue: 0.1736 time to fit residues: 150.6376 Evaluate side-chains 460 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 397 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU 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 A residue 455 MET Chi-restraints excluded: chain C residue 42 VAL 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 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE 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 720 ILE 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 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 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 366 SER 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 658 ASN Chi-restraints excluded: chain B residue 723 THR 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 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 291 CYS Chi-restraints excluded: chain D residue 338 PHE 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 610 VAL Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 762 GLN 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 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: 0.9980 chunk 115 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 139 optimal weight: 0.0670 chunk 134 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 239 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN B 314 GLN B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 ASN D 762 GLN D 777 ASN D1011 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.148607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.125280 restraints weight = 101857.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.126458 restraints weight = 77592.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.127815 restraints weight = 55477.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.127472 restraints weight = 47507.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.127395 restraints weight = 40945.410| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31748 Z= 0.137 Angle : 0.664 24.130 43327 Z= 0.319 Chirality : 0.046 0.450 5018 Planarity : 0.004 0.051 5481 Dihedral : 4.495 28.885 4071 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Rotamer: Outliers : 2.59 % Allowed : 13.77 % Favored : 83.64 % 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: -0.80 (0.13), residues: 3760 helix: 0.27 (0.16), residues: 1015 sheet: -0.44 (0.17), residues: 705 loop : -0.94 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 115 TYR 0.022 0.002 TYR B1138 PHE 0.028 0.002 PHE A 230 TRP 0.033 0.001 TRP A 566 HIS 0.008 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (31633) covalent geometry : angle 0.61077 / 0.31 (43027) SS BOND : bond 0.00553 / 0.41 ( 42) SS BOND : angle 2.26387 / 1.54 ( 84) hydrogen bonds : bond 0.04374 / 2.90 ( 1149) hydrogen bonds : angle 5.95227 / 4.17 ( 3228) Misc. bond : bond 0.00006 / 0.00 ( 1) link_BETA1-4 : bond 0.01155 / 0.60 ( 18) link_BETA1-4 : angle 3.76096 / 2.73 ( 54) link_NAG-ASN : bond 0.00538 / 0.34 ( 54) link_NAG-ASN : angle 3.38240 / 2.51 ( 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 530 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 444 time to evaluate : 1.155 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: 0.5849 (t80) cc_final: 0.5204 (t80) REVERT: A 45 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.4941 (mt) REVERT: A 190 MET cc_start: 0.3735 (ptp) cc_final: 0.3379 (ttt) REVERT: A 360 MET cc_start: 0.4468 (ttp) cc_final: 0.3871 (ptm) REVERT: A 428 PHE cc_start: 0.5755 (m-80) cc_final: 0.5401 (m-80) REVERT: A 472 GLN cc_start: 0.6338 (pt0) cc_final: 0.5844 (mm-40) REVERT: A 518 ARG cc_start: 0.4843 (ppt170) cc_final: 0.4581 (ppt170) REVERT: A 564 GLU cc_start: 0.6022 (tp30) cc_final: 0.4593 (mt-10) REVERT: C 240 THR cc_start: 0.7785 (m) cc_final: 0.7580 (p) REVERT: C 614 ASP cc_start: 0.6207 (t0) cc_final: 0.5674 (t0) REVERT: C 698 SER cc_start: 0.8397 (t) cc_final: 0.7949 (p) REVERT: C 741 TYR cc_start: 0.8210 (t80) cc_final: 0.7709 (t80) REVERT: C 775 ASP cc_start: 0.7080 (m-30) cc_final: 0.6877 (m-30) REVERT: C 780 GLU cc_start: 0.7514 (pt0) cc_final: 0.6880 (pt0) REVERT: C 819 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6639 (mt-10) REVERT: C 901 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8189 (tp40) REVERT: C 959 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8498 (mp) REVERT: C 962 LEU cc_start: 0.8933 (tp) cc_final: 0.8326 (tp) REVERT: C 1019 ARG cc_start: 0.7850 (tpt90) cc_final: 0.7398 (tpt170) REVERT: B 231 ILE cc_start: 0.6259 (mt) cc_final: 0.5875 (mm) REVERT: B 500 THR cc_start: 0.5995 (p) cc_final: 0.5349 (t) REVERT: B 551 VAL cc_start: 0.7834 (t) cc_final: 0.7287 (p) REVERT: B 731 MET cc_start: 0.8134 (ttp) cc_final: 0.7795 (ptm) REVERT: B 737 ASP cc_start: 0.6817 (t0) cc_final: 0.6564 (t0) REVERT: B 1029 MET cc_start: 0.8101 (tpp) cc_final: 0.7863 (tpp) REVERT: D 396 TYR cc_start: 0.5791 (m-80) cc_final: 0.5311 (m-10) REVERT: D 869 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7651 (ttm) REVERT: D 902 MET cc_start: 0.8640 (mmm) cc_final: 0.8066 (mmt) REVERT: D 914 ASN cc_start: 0.7740 (p0) cc_final: 0.7448 (p0) REVERT: D 1003 SER cc_start: 0.9203 (p) cc_final: 0.8987 (m) outliers start: 86 outliers final: 57 residues processed: 498 average time/residue: 0.1743 time to fit residues: 143.8602 Evaluate side-chains 446 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 385 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 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 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 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 714 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 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 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 342 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 723 THR 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 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 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 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 610 VAL Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 869 MET 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: 5.9990 chunk 5 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 262 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 522 GLN ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN C 30 ASN C 245 HIS C 394 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN B 314 GLN B 448 ASN B 658 ASN D 536 ASN D 965 GLN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.137060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.115432 restraints weight = 109558.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.116666 restraints weight = 79221.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.116717 restraints weight = 53368.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.116963 restraints weight = 48003.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.117029 restraints weight = 48190.376| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 31748 Z= 0.283 Angle : 0.852 20.317 43327 Z= 0.418 Chirality : 0.052 0.437 5018 Planarity : 0.005 0.052 5481 Dihedral : 5.300 23.107 4071 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 3.43 % Allowed : 13.71 % Favored : 82.86 % 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: -1.33 (0.12), residues: 3760 helix: -0.18 (0.16), residues: 1011 sheet: -0.68 (0.18), residues: 672 loop : -1.30 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 115 TYR 0.030 0.003 TYR B 369 PHE 0.027 0.003 PHE C 817 TRP 0.032 0.003 TRP A 566 HIS 0.009 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.28 (31633) covalent geometry : angle 0.81122 / 0.41 (43027) SS BOND : bond 0.01013 / 0.64 ( 42) SS BOND : angle 2.23281 / 1.54 ( 84) hydrogen bonds : bond 0.04951 / 3.30 ( 1149) hydrogen bonds : angle 6.42540 / 4.51 ( 3228) Misc. bond : bond 0.00030 / 0.02 ( 1) link_BETA1-4 : bond 0.01204 / 0.64 ( 18) link_BETA1-4 : angle 3.93464 / 2.84 ( 54) link_NAG-ASN : bond 0.00863 / 0.58 ( 54) link_NAG-ASN : angle 3.41904 / 2.53 ( 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 540 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 426 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.5239 (OUTLIER) cc_final: 0.4621 (mt) REVERT: A 168 TRP cc_start: 0.1405 (t-100) cc_final: -0.0125 (t60) REVERT: A 190 MET cc_start: 0.3834 (ptp) cc_final: 0.3538 (ttt) REVERT: A 270 MET cc_start: 0.0444 (mtm) cc_final: 0.0099 (mtm) REVERT: A 360 MET cc_start: 0.4596 (ttp) cc_final: 0.4295 (ptm) REVERT: A 592 PHE cc_start: 0.3874 (t80) cc_final: 0.3580 (t80) REVERT: C 269 TYR cc_start: 0.5661 (OUTLIER) cc_final: 0.5210 (m-10) REVERT: C 392 PHE cc_start: 0.7183 (m-80) cc_final: 0.6892 (m-80) REVERT: C 614 ASP cc_start: 0.6126 (t0) cc_final: 0.5660 (t0) REVERT: C 698 SER cc_start: 0.8613 (t) cc_final: 0.8284 (m) REVERT: C 741 TYR cc_start: 0.8301 (t80) cc_final: 0.8052 (t80) REVERT: C 780 GLU cc_start: 0.7295 (pt0) cc_final: 0.6658 (pt0) REVERT: C 901 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: C 904 TYR cc_start: 0.6784 (p90) cc_final: 0.6474 (p90) REVERT: C 931 ILE cc_start: 0.8794 (mm) cc_final: 0.8240 (mm) REVERT: C 959 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8636 (mp) REVERT: C 962 LEU cc_start: 0.9091 (tp) cc_final: 0.8347 (tp) REVERT: C 1017 GLU cc_start: 0.7282 (tt0) cc_final: 0.7005 (tt0) REVERT: C 1019 ARG cc_start: 0.7797 (tpt90) cc_final: 0.7585 (tpt170) REVERT: B 231 ILE cc_start: 0.6355 (mt) cc_final: 0.6070 (mm) REVERT: B 1019 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7169 (tpt90) REVERT: D 54 LEU cc_start: 0.6394 (mt) cc_final: 0.5722 (mp) REVERT: D 378 LYS cc_start: 0.5566 (OUTLIER) cc_final: 0.5128 (pttm) REVERT: D 396 TYR cc_start: 0.6108 (m-80) cc_final: 0.5792 (m-10) REVERT: D 440 ASN cc_start: 0.7704 (m-40) cc_final: 0.7389 (t0) REVERT: D 536 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6766 (t0) REVERT: D 902 MET cc_start: 0.8796 (mmm) cc_final: 0.8203 (mmt) REVERT: D 904 TYR cc_start: 0.6997 (t80) cc_final: 0.6596 (t80) REVERT: D 1102 TRP cc_start: 0.7611 (m100) cc_final: 0.7406 (m100) outliers start: 114 outliers final: 79 residues processed: 500 average time/residue: 0.1935 time to fit residues: 159.5178 Evaluate side-chains 440 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 355 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 327 PHE Chi-restraints excluded: chain A residue 373 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 120 VAL 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 382 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 516 GLU 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 664 ILE Chi-restraints excluded: chain C residue 719 THR 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 849 LEU 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 963 VAL Chi-restraints excluded: chain C residue 966 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 88 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU 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 342 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 658 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 761 THR 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 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain D residue 51 THR 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 513 LEU Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 735 SER Chi-restraints excluded: chain D residue 752 LEU 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 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 1040 VAL Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1146 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 174 optimal weight: 0.7980 chunk 336 optimal weight: 0.9980 chunk 172 optimal weight: 20.0000 chunk 140 optimal weight: 0.0270 chunk 159 optimal weight: 0.8980 chunk 354 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 249 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 258 optimal weight: 0.3980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 965 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 501 ASN B 658 ASN D 536 ASN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.144683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.122306 restraints weight = 104069.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.123019 restraints weight = 77124.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.122400 restraints weight = 69190.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.122652 restraints weight = 65371.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.122717 restraints weight = 56870.002| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31748 Z= 0.145 Angle : 0.711 20.455 43327 Z= 0.347 Chirality : 0.046 0.393 5018 Planarity : 0.004 0.051 5481 Dihedral : 4.894 22.162 4071 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 2.41 % Allowed : 15.69 % Favored : 81.90 % 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: -1.09 (0.13), residues: 3760 helix: 0.09 (0.16), residues: 1007 sheet: -0.61 (0.18), residues: 689 loop : -1.15 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 115 TYR 0.021 0.002 TYR B1138 PHE 0.030 0.002 PHE C 817 TRP 0.044 0.002 TRP B 886 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (31633) covalent geometry : angle 0.66769 / 0.34 (43027) SS BOND : bond 0.00494 / 0.32 ( 42) SS BOND : angle 2.67937 / 1.97 ( 84) hydrogen bonds : bond 0.04356 / 2.92 ( 1149) hydrogen bonds : angle 6.11231 / 4.26 ( 3228) Misc. bond : bond 0.00009 / 0.00 ( 1) link_BETA1-4 : bond 0.01032 / 0.56 ( 18) link_BETA1-4 : angle 3.27881 / 2.28 ( 54) link_NAG-ASN : bond 0.00560 / 0.34 ( 54) link_NAG-ASN : angle 3.08846 / 2.29 ( 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 498 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 418 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.4114 (t80) cc_final: 0.3477 (t80) REVERT: A 45 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.4691 (mt) REVERT: A 168 TRP cc_start: 0.1118 (t-100) cc_final: -0.0284 (t60) REVERT: A 190 MET cc_start: 0.4073 (ptp) cc_final: 0.3725 (ttt) REVERT: A 270 MET cc_start: 0.0548 (mtm) cc_final: 0.0288 (mtm) REVERT: A 327 PHE cc_start: 0.5231 (t80) cc_final: 0.4493 (t80) REVERT: A 518 ARG cc_start: 0.4461 (tmm160) cc_final: 0.3823 (ptm-80) REVERT: A 592 PHE cc_start: 0.3774 (t80) cc_final: 0.3488 (t80) REVERT: C 380 TYR cc_start: 0.6028 (m-80) cc_final: 0.3647 (m-10) REVERT: C 614 ASP cc_start: 0.6208 (t0) cc_final: 0.5702 (t0) REVERT: C 698 SER cc_start: 0.8628 (t) cc_final: 0.8339 (m) REVERT: C 741 TYR cc_start: 0.8164 (t80) cc_final: 0.7633 (t80) REVERT: C 780 GLU cc_start: 0.7382 (pt0) cc_final: 0.6865 (pt0) REVERT: C 901 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8200 (tp40) REVERT: C 959 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8636 (mp) REVERT: C 962 LEU cc_start: 0.8908 (tp) cc_final: 0.8373 (tp) REVERT: C 1005 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7968 (mm110) REVERT: B 231 ILE cc_start: 0.6364 (mt) cc_final: 0.6041 (mm) REVERT: B 298 GLU cc_start: 0.7678 (tp30) cc_final: 0.7391 (tp30) REVERT: B 387 LEU cc_start: 0.5292 (tp) cc_final: 0.4843 (tp) REVERT: B 551 VAL cc_start: 0.7668 (t) cc_final: 0.7137 (p) REVERT: B 707 TYR cc_start: 0.7365 (t80) cc_final: 0.6200 (m-80) REVERT: B 1019 ARG cc_start: 0.7747 (tpp-160) cc_final: 0.7139 (tpt90) REVERT: D 54 LEU cc_start: 0.5486 (mt) cc_final: 0.4731 (mp) REVERT: D 378 LYS cc_start: 0.5593 (OUTLIER) cc_final: 0.5388 (pttm) REVERT: D 398 ASP cc_start: 0.5722 (m-30) cc_final: 0.5351 (t0) REVERT: D 494 SER cc_start: 0.4487 (p) cc_final: 0.4171 (p) REVERT: D 536 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.7011 (t0) REVERT: D 731 MET cc_start: 0.8389 (ptm) cc_final: 0.8111 (ptm) REVERT: D 740 MET cc_start: 0.6124 (mmm) cc_final: 0.5648 (mtp) REVERT: D 774 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7853 (mm-40) REVERT: D 902 MET cc_start: 0.8703 (mmm) cc_final: 0.8150 (mmt) REVERT: D 950 ASP cc_start: 0.7216 (m-30) cc_final: 0.6938 (m-30) outliers start: 80 outliers final: 49 residues processed: 470 average time/residue: 0.1916 time to fit residues: 148.8560 Evaluate side-chains 432 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 378 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 51 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 495 TYR 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 709 ASN Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE 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 B residue 83 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 342 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 658 ASN 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 761 THR 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 1001 LEU Chi-restraints excluded: chain D residue 51 THR 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 513 LEU Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 673 SER 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 1006 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 103 optimal weight: 0.0570 chunk 135 optimal weight: 4.9990 chunk 371 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 955 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 953 ASN D 536 ASN ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.143002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.120629 restraints weight = 105521.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.121352 restraints weight = 87112.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.121274 restraints weight = 65569.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.121346 restraints weight = 70374.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.121374 restraints weight = 56250.620| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31748 Z= 0.175 Angle : 0.708 19.824 43327 Z= 0.347 Chirality : 0.047 0.421 5018 Planarity : 0.004 0.057 5481 Dihedral : 4.912 25.820 4071 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 2.50 % Allowed : 16.27 % Favored : 81.24 % 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: -1.10 (0.13), residues: 3760 helix: 0.13 (0.16), residues: 1015 sheet: -0.53 (0.18), residues: 643 loop : -1.22 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 115 TYR 0.045 0.002 TYR B 396 PHE 0.020 0.002 PHE D 201 TRP 0.048 0.002 TRP B 886 HIS 0.009 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (31633) covalent geometry : angle 0.66858 / 0.34 (43027) SS BOND : bond 0.00419 / 0.27 ( 42) SS BOND : angle 2.24871 / 1.66 ( 84) hydrogen bonds : bond 0.04313 / 2.88 ( 1149) hydrogen bonds : angle 6.04826 / 4.22 ( 3228) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-4 : bond 0.01135 / 0.60 ( 18) link_BETA1-4 : angle 3.17151 / 2.18 ( 54) link_NAG-ASN : bond 0.00572 / 0.35 ( 54) link_NAG-ASN : angle 3.05958 / 2.29 ( 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 489 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 406 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.3935 (t80) cc_final: 0.3340 (t80) REVERT: A 45 LEU cc_start: 0.5268 (OUTLIER) cc_final: 0.4641 (mt) REVERT: A 168 TRP cc_start: 0.1230 (t-100) cc_final: -0.0296 (t60) REVERT: A 190 MET cc_start: 0.4012 (ptp) cc_final: 0.3647 (ttt) REVERT: A 327 PHE cc_start: 0.5248 (t80) cc_final: 0.4442 (t80) REVERT: A 592 PHE cc_start: 0.4052 (t80) cc_final: 0.3652 (t80) REVERT: C 104 TRP cc_start: 0.5519 (OUTLIER) cc_final: 0.5073 (m100) REVERT: C 380 TYR cc_start: 0.5940 (m-80) cc_final: 0.3686 (m-10) REVERT: C 614 ASP cc_start: 0.6101 (t0) cc_final: 0.5275 (t0) REVERT: C 698 SER cc_start: 0.8691 (t) cc_final: 0.8160 (p) REVERT: C 901 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7918 (tp40) REVERT: C 959 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8661 (mp) REVERT: C 962 LEU cc_start: 0.8918 (tp) cc_final: 0.8292 (tp) REVERT: C 1029 MET cc_start: 0.8892 (tpp) cc_final: 0.8567 (tpt) REVERT: B 231 ILE cc_start: 0.6347 (mt) cc_final: 0.5955 (mm) REVERT: B 387 LEU cc_start: 0.5399 (tp) cc_final: 0.5145 (tp) REVERT: B 551 VAL cc_start: 0.7738 (t) cc_final: 0.7166 (p) REVERT: D 54 LEU cc_start: 0.5285 (mt) cc_final: 0.4475 (mp) REVERT: D 378 LYS cc_start: 0.5596 (OUTLIER) cc_final: 0.5271 (pttm) REVERT: D 398 ASP cc_start: 0.5663 (m-30) cc_final: 0.5329 (t0) REVERT: D 536 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6706 (t0) REVERT: D 737 ASP cc_start: 0.6365 (p0) cc_final: 0.5222 (p0) REVERT: D 740 MET cc_start: 0.5996 (mmm) cc_final: 0.5699 (mtp) REVERT: D 774 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7675 (mm-40) REVERT: D 902 MET cc_start: 0.8685 (mmm) cc_final: 0.8053 (mmt) REVERT: D 1031 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7401 (mp0) outliers start: 83 outliers final: 62 residues processed: 460 average time/residue: 0.1873 time to fit residues: 143.8182 Evaluate side-chains 438 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 369 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 495 TYR 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 709 ASN Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE 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 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 88 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 342 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 658 ASN 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 761 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 154 GLU Chi-restraints excluded: chain D residue 241 LEU 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 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 536 ASN Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 673 SER 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 996 LEU Chi-restraints excluded: chain D residue 1006 THR Chi-restraints excluded: chain D residue 1031 GLU Chi-restraints excluded: chain D residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 240 optimal weight: 0.3980 chunk 214 optimal weight: 0.9980 chunk 320 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 949 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN ** D 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.132515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.113153 restraints weight = 117228.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.114120 restraints weight = 75452.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.114266 restraints weight = 50167.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.114444 restraints weight = 45302.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.114597 restraints weight = 43787.640| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 31748 Z= 0.145 Angle : 0.676 19.544 43327 Z= 0.332 Chirality : 0.046 0.405 5018 Planarity : 0.004 0.060 5481 Dihedral : 4.793 23.672 4071 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.91 % Favored : 95.98 % Rotamer: Outliers : 2.35 % Allowed : 16.93 % Favored : 80.73 % 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: -1.05 (0.13), residues: 3760 helix: 0.15 (0.16), residues: 1021 sheet: -0.46 (0.18), residues: 646 loop : -1.20 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 115 TYR 0.036 0.002 TYR B 396 PHE 0.022 0.002 PHE C 329 TRP 0.033 0.002 TRP A 566 HIS 0.009 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (31633) covalent geometry : angle 0.63977 / 0.32 (43027) SS BOND : bond 0.00382 / 0.26 ( 42) SS BOND : angle 2.00024 / 1.47 ( 84) hydrogen bonds : bond 0.04158 / 2.78 ( 1149) hydrogen bonds : angle 5.96105 / 4.15 ( 3228) Misc. bond : bond 0.00007 / 0.00 ( 1) link_BETA1-4 : bond 0.01005 / 0.54 ( 18) link_BETA1-4 : angle 2.98279 / 2.01 ( 54) link_NAG-ASN : bond 0.00511 / 0.31 ( 54) link_NAG-ASN : angle 2.93507 / 2.20 ( 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 488 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 410 time to evaluate : 1.153 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: A 32 PHE cc_start: 0.3939 (t80) cc_final: 0.3593 (t80) REVERT: A 45 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.4660 (mt) REVERT: A 168 TRP cc_start: 0.1205 (t-100) cc_final: -0.0311 (t60) REVERT: A 190 MET cc_start: 0.3896 (ptp) cc_final: 0.3581 (ttt) REVERT: A 327 PHE cc_start: 0.4809 (t80) cc_final: 0.3975 (t80) REVERT: A 472 GLN cc_start: 0.5961 (pt0) cc_final: 0.5271 (mm-40) REVERT: A 592 PHE cc_start: 0.4166 (t80) cc_final: 0.3697 (t80) REVERT: C 104 TRP cc_start: 0.5611 (OUTLIER) cc_final: 0.5101 (m100) REVERT: C 380 TYR cc_start: 0.6023 (m-80) cc_final: 0.3655 (m-10) REVERT: C 614 ASP cc_start: 0.6118 (t0) cc_final: 0.5239 (t0) REVERT: C 698 SER cc_start: 0.8782 (t) cc_final: 0.8129 (p) REVERT: C 780 GLU cc_start: 0.7131 (pt0) cc_final: 0.6663 (pt0) REVERT: C 901 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8068 (tp40) REVERT: C 959 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 962 LEU cc_start: 0.8870 (tp) cc_final: 0.8474 (tp) REVERT: C 1019 ARG cc_start: 0.7856 (tpt170) cc_final: 0.7436 (tpt170) REVERT: B 551 VAL cc_start: 0.7994 (t) cc_final: 0.7443 (p) REVERT: B 707 TYR cc_start: 0.7177 (t80) cc_final: 0.6277 (m-80) REVERT: B 1019 ARG cc_start: 0.8283 (tpm170) cc_final: 0.7282 (tpt90) REVERT: D 54 LEU cc_start: 0.5642 (mt) cc_final: 0.5383 (mp) REVERT: D 398 ASP cc_start: 0.5722 (m-30) cc_final: 0.5194 (t0) REVERT: D 400 PHE cc_start: 0.4997 (p90) cc_final: 0.4525 (p90) REVERT: D 439 ASN cc_start: 0.6034 (t0) cc_final: 0.5797 (t0) REVERT: D 740 MET cc_start: 0.5886 (mmm) cc_final: 0.5538 (mtp) REVERT: D 774 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7579 (mm-40) REVERT: D 902 MET cc_start: 0.8671 (mmm) cc_final: 0.8111 (mmt) REVERT: D 1031 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7304 (mp0) outliers start: 78 outliers final: 59 residues processed: 462 average time/residue: 0.1816 time to fit residues: 139.7541 Evaluate side-chains 436 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 372 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 495 TYR 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 709 ASN Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 856 ASN 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 966 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 223 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 342 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 581 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 658 ASN 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 866 THR Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain D residue 51 THR 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 536 ASN 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 878 LEU Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1031 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 78 optimal weight: 0.0980 chunk 223 optimal weight: 2.9990 chunk 335 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 658 ASN B 953 ASN D 536 ASN D 777 ASN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.132585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.112844 restraints weight = 116784.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.114378 restraints weight = 70203.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.114596 restraints weight = 45322.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.114917 restraints weight = 34217.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.115056 restraints weight = 32712.058| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.6553 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= 0.147 Angle : 0.685 19.182 43327 Z= 0.334 Chirality : 0.046 0.401 5018 Planarity : 0.004 0.061 5481 Dihedral : 4.782 25.664 4071 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 2.22 % Allowed : 17.41 % Favored : 80.37 % 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: -1.02 (0.13), residues: 3760 helix: 0.21 (0.16), residues: 1020 sheet: -0.47 (0.18), residues: 651 loop : -1.19 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 115 TYR 0.033 0.002 TYR C 904 PHE 0.021 0.002 PHE C 329 TRP 0.048 0.002 TRP C 886 HIS 0.009 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (31633) covalent geometry : angle 0.65040 / 0.33 (43027) SS BOND : bond 0.00464 / 0.32 ( 42) SS BOND : angle 1.94237 / 1.48 ( 84) hydrogen bonds : bond 0.04125 / 2.75 ( 1149) hydrogen bonds : angle 5.91452 / 4.11 ( 3228) Misc. bond : bond 0.00013 / 0.01 ( 1) link_BETA1-4 : bond 0.01033 / 0.56 ( 18) link_BETA1-4 : angle 2.96607 / 2.00 ( 54) link_NAG-ASN : bond 0.00456 / 0.26 ( 54) link_NAG-ASN : angle 2.86608 / 2.14 ( 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 478 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 404 time to evaluate : 1.203 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: A 32 PHE cc_start: 0.4340 (t80) cc_final: 0.4049 (t80) REVERT: A 45 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4684 (mt) REVERT: A 168 TRP cc_start: 0.1155 (t-100) cc_final: -0.0327 (t60) REVERT: A 190 MET cc_start: 0.4149 (ptp) cc_final: 0.3678 (ttt) REVERT: A 199 TYR cc_start: 0.0398 (t80) cc_final: -0.0160 (t80) REVERT: A 327 PHE cc_start: 0.4787 (t80) cc_final: 0.4065 (t80) REVERT: A 472 GLN cc_start: 0.5930 (pt0) cc_final: 0.5345 (mm-40) REVERT: A 592 PHE cc_start: 0.4073 (t80) cc_final: 0.3739 (t80) REVERT: C 104 TRP cc_start: 0.5702 (OUTLIER) cc_final: 0.5055 (m100) REVERT: C 380 TYR cc_start: 0.5970 (m-80) cc_final: 0.3595 (m-10) REVERT: C 495 TYR cc_start: 0.4241 (OUTLIER) cc_final: 0.3927 (m-80) REVERT: C 614 ASP cc_start: 0.6063 (t0) cc_final: 0.5482 (t70) REVERT: C 780 GLU cc_start: 0.7075 (pt0) cc_final: 0.6860 (pt0) REVERT: C 901 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8004 (tp40) REVERT: C 959 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8695 (mp) REVERT: C 962 LEU cc_start: 0.8872 (tp) cc_final: 0.8388 (tp) REVERT: C 1019 ARG cc_start: 0.7835 (tpt170) cc_final: 0.7476 (tpt170) REVERT: C 1029 MET cc_start: 0.8876 (tpp) cc_final: 0.8254 (tpt) REVERT: B 551 VAL cc_start: 0.8027 (t) cc_final: 0.7483 (p) REVERT: B 707 TYR cc_start: 0.7194 (t80) cc_final: 0.6294 (m-80) REVERT: B 1019 ARG cc_start: 0.8286 (tpm170) cc_final: 0.7462 (tpt90) REVERT: D 54 LEU cc_start: 0.5723 (mt) cc_final: 0.5448 (mp) REVERT: D 398 ASP cc_start: 0.5665 (m-30) cc_final: 0.5158 (t0) REVERT: D 400 PHE cc_start: 0.4905 (p90) cc_final: 0.4450 (p90) REVERT: D 439 ASN cc_start: 0.6025 (t0) cc_final: 0.5540 (m-40) REVERT: D 740 MET cc_start: 0.5872 (mmm) cc_final: 0.5589 (mtp) REVERT: D 902 MET cc_start: 0.8653 (mmm) cc_final: 0.8096 (mmt) REVERT: D 1031 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7242 (mp0) outliers start: 74 outliers final: 59 residues processed: 448 average time/residue: 0.1823 time to fit residues: 135.9078 Evaluate side-chains 441 residues out of total 3326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 376 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 495 TYR 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 709 ASN Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 856 ASN 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 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 223 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 342 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 581 THR Chi-restraints excluded: chain B residue 658 ASN 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 866 THR Chi-restraints excluded: chain B residue 920 GLN Chi-restraints excluded: chain B residue 953 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 241 LEU 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 449 TYR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 536 ASN 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 915 VAL Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1031 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 331 optimal weight: 0.5980 chunk 315 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 347 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.132620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.113064 restraints weight = 119048.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.114186 restraints weight = 75889.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.114366 restraints weight = 53389.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.114805 restraints weight = 41042.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.114945 restraints weight = 36167.708| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 31748 Z= 0.224 Angle : 0.919 59.191 43327 Z= 0.500 Chirality : 0.049 0.661 5018 Planarity : 0.005 0.129 5481 Dihedral : 4.825 28.503 4071 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 2.13 % Allowed : 17.77 % Favored : 80.10 % Cbeta Deviations : 0.20 % 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: 0.20 (0.16), residues: 1020 sheet: -0.46 (0.18), residues: 648 loop : -1.18 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.001 ARG C 237 TYR 0.055 0.002 TYR B 396 PHE 0.042 0.002 PHE C 306 TRP 0.041 0.002 TRP C 886 HIS 0.006 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (31633) covalent geometry : angle 0.86293 / 0.48 (43027) SS BOND : bond 0.00831 / 0.39 ( 42) SS BOND : angle 5.03787 / 3.09 ( 84) hydrogen bonds : bond 0.04221 / 2.79 ( 1149) hydrogen bonds : angle 5.92865 / 4.12 ( 3228) Misc. bond : bond 0.00013 / 0.01 ( 1) link_BETA1-4 : bond 0.00968 / 0.52 ( 18) link_BETA1-4 : angle 2.98209 / 2.02 ( 54) link_NAG-ASN : bond 0.00441 / 0.25 ( 54) link_NAG-ASN : angle 3.45031 / 2.46 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6122.12 seconds wall clock time: 106 minutes 32.67 seconds (6392.67 seconds total)