Starting phenix.real_space_refine on Mon Sep 14 12:42:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u6i_20666/09_2026/6u6i_20666.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u6i_20666/09_2026/6u6i_20666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6u6i_20666/09_2026/6u6i_20666.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u6i_20666/09_2026/6u6i_20666.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u6i_20666/09_2026/6u6i_20666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u6i_20666/09_2026/6u6i_20666.map" model { file = "/net/cci-nas-00/data/ceres_data/6u6i_20666/09_2026/6u6i_20666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u6i_20666/09_2026/6u6i_20666.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10696 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 7261 2.51 5 N 1872 2.21 5 O 2195 1.98 5 H 10337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21701 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 5239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 5239 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 9, 'GLN:plan1': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 5327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 5327 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 10, 'ASP:plan': 6, 'GLU:plan': 13, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 5410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 5410 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 146 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 10, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 5577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 5577 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.51, per 1000 atoms: 0.16 Number of scatterers: 21701 At special positions: 0 Unit cell: (138.58, 125.788, 91.676, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 2195 8.00 N 1872 7.00 C 7261 6.00 H 10337 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " 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=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 904 " - " ASN B 355 " " NAG E 1 " - " ASN C 241 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN B 241 " " NAG H 1 " - " ASN D 241 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 662.0 milliseconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 15 sheets defined 39.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.711A pdb=" N ILE C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 172 through 185 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 252 through 265 removed outlier: 3.945A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.511A pdb=" N ALA C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 334 removed outlier: 4.266A pdb=" N VAL C 327 " --> pdb=" O TRP C 323 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 329 " --> pdb=" O GLN C 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 4.028A pdb=" N TYR A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.735A pdb=" N ILE A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 174 through 188 removed outlier: 3.633A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.823A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 37 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.692A pdb=" N ILE B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 174 through 187 removed outlier: 3.531A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.831A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 301 Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.626A pdb=" N ILE B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 removed outlier: 4.041A pdb=" N ILE D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 172 through 188 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.506A pdb=" N SER D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.055A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 50 removed outlier: 4.735A pdb=" N ALA C 72 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.678A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR C 220 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N PHE C 245 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE C 222 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE C 358 " --> pdb=" O TYR C 373 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR C 373 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 360 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 337 through 340 removed outlier: 3.638A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 50 removed outlier: 7.410A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 164 removed outlier: 6.705A pdb=" N PHE A 133 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE A 193 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.702A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 47 removed outlier: 8.936A pdb=" N PHE B 74 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.516A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 164 removed outlier: 9.019A pdb=" N ILE B 193 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA B 134 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASP B 195 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 136 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 222 removed outlier: 6.288A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 337 through 340 removed outlier: 4.058A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 49 Processing sheet with id=AB4, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.287A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS D 364 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 340 539 hydrogen bonds defined for protein. 1593 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: 4.61 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10329 1.03 - 1.23: 19 1.23 - 1.42: 5026 1.42 - 1.62: 6518 1.62 - 1.81: 56 Bond restraints: 21948 Sorted by residual: bond pdb=" CG PRO D 99 " pdb=" CD PRO D 99 " ideal model delta sigma weight residual 1.503 1.458 0.045 3.40e-02 8.65e+02 1.77e+00 bond pdb=" C1 NAG B 904 " pdb=" O5 NAG B 904 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" CG LEU D 136 " pdb=" CD2 LEU D 136 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CG PRO C 99 " pdb=" CD PRO C 99 " ideal model delta sigma weight residual 1.503 1.461 0.042 3.40e-02 8.65e+02 1.52e+00 bond pdb=" C5 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.38e+00 ... (remaining 21943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 38218 1.27 - 2.54: 976 2.54 - 3.81: 63 3.81 - 5.08: 11 5.08 - 6.35: 4 Bond angle restraints: 39272 Sorted by residual: angle pdb=" N VAL A 165 " pdb=" CA VAL A 165 " pdb=" C VAL A 165 " ideal model delta sigma weight residual 113.71 110.53 3.18 9.50e-01 1.11e+00 1.12e+01 angle pdb=" CA VAL A 165 " pdb=" C VAL A 165 " pdb=" N GLY A 166 " ideal model delta sigma weight residual 119.87 116.84 3.03 1.34e+00 5.57e-01 5.10e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.60 6.35 3.00e+00 1.11e-01 4.48e+00 angle pdb=" C3 BMA G 3 " pdb=" C2 BMA G 3 " pdb=" O2 BMA G 3 " ideal model delta sigma weight residual 112.95 106.65 6.30 3.00e+00 1.11e-01 4.41e+00 angle pdb=" N THR A 98 " pdb=" CA THR A 98 " pdb=" C THR A 98 " ideal model delta sigma weight residual 107.95 112.32 -4.37 2.14e+00 2.18e-01 4.18e+00 ... (remaining 39267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 9566 17.47 - 34.93: 680 34.93 - 52.40: 152 52.40 - 69.86: 58 69.86 - 87.33: 3 Dihedral angle restraints: 10459 sinusoidal: 5270 harmonic: 5189 Sorted by residual: dihedral pdb=" CB CYS D 63 " pdb=" SG CYS D 63 " pdb=" SG CYS D 315 " pdb=" CB CYS D 315 " ideal model delta sinusoidal sigma weight residual -86.00 -43.63 -42.37 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CA THR D 38 " pdb=" C THR D 38 " pdb=" N SER D 39 " pdb=" CA SER D 39 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LYS D 364 " pdb=" CB LYS D 364 " pdb=" CG LYS D 364 " pdb=" CD LYS D 364 " ideal model delta sinusoidal sigma weight residual 180.00 131.39 48.61 3 1.50e+01 4.44e-03 8.66e+00 ... (remaining 10456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 1851 0.328 - 0.656: 3 0.656 - 0.984: 0 0.984 - 1.313: 0 1.313 - 1.641: 2 Chirality restraints: 1856 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-02 2.50e+03 6.73e+03 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.07 -1.33 2.00e-02 2.50e+03 4.45e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-02 2.50e+03 4.05e+02 ... (remaining 1853 not shown) Planarity restraints: 3496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 44 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO D 45 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 45 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 45 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 18 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO C 19 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 19 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 19 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 18 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO A 19 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " -0.020 5.00e-02 4.00e+02 ... (remaining 3493 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1246 2.19 - 2.79: 44378 2.79 - 3.40: 56647 3.40 - 4.00: 76201 4.00 - 4.60: 118764 Nonbonded interactions: 297236 Sorted by model distance: nonbonded pdb=" O GLU B 266 " pdb=" H GLU B 269 " model vdw 1.588 2.450 nonbonded pdb=" OD1 ASP A 252 " pdb=" H VAL A 255 " model vdw 1.592 2.450 nonbonded pdb=" HH TYR D 77 " pdb=" O PHE D 101 " model vdw 1.605 2.450 nonbonded pdb=" O GLU A 260 " pdb=" HG1 THR A 264 " model vdw 1.610 2.450 nonbonded pdb=" O ASN B 344 " pdb="HH21 ARG B 353 " model vdw 1.618 2.450 ... (remaining 297231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 45 through 53 or (resid \ 54 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 55 through 78 or (resid 79 through 80 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 81 through 131 or (resid \ 132 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 133 through 140 or (resid 141 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 142 through 155 or (resid 156 th \ rough 157 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 158 through 182 or (resid 183 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA )) \ or (resid 184 through 190 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 191 through 199 or (resid 200 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 201 throug \ h 230 or (resid 231 through 232 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 233 or (resid 234 through 236 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 237 \ through 256 or (resid 257 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 258 through 265 or (resid 266 through 269 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 270 through 273 or (resid 274 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 275 through 278 or (resid 279 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 280 \ through 296 or (resid 297 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 298 through 301 or (resid 302 through 303 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 304 through 333 or (resid 334 through 335 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 336 through 343 or (resid 344 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name H or name HA )) or resid 345 or (resid 346 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 347 through \ 351 or (resid 352 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 353 through 383)) selection = (chain 'B' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 14 through 22 or (resid \ 23 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 24 through 43 or (resid 44 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 45 through 47 or (resid 48 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 49 \ through 103 or (resid 104 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 105 through 115 or (resid 116 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 117 throu \ gh 139 or (resid 140 through 141 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 142 through 155 or (resid 156 through 15 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 158 through 169 or (resid 170 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 171 through 177 or (resid 178 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 179 through 182 or (resid 183 and (name N or name CA or name C or name O or n \ ame CB or name CG or name OD1 or name OD2 or name H or name HA )) or (resid 184 \ through 190 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 191 through 197 or (resid 198 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA )) or resid 199 or (resid 200 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 201 through \ 205 or (resid 206 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 207 through 212 or (resid 213 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 214 through 215 o \ r (resid 216 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 217 through 230 or (resid 231 through 232 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 233 or (res \ id 234 through 236 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 237 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 275 through 278 o \ r (resid 279 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 280 through 293 or (resid 294 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 295 through 298 or (res \ id 299 through 303 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 304 through 305 or (resid 306 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 307 through 333 o \ r (resid 334 through 335 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 336 through 343 or (resid 344 and (name N or nam \ e CA or name C or name O or name CB or name CG or name OD1 or name ND2 or name H \ or name HA )) or resid 345 through 361 or (resid 362 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 363 through 368 or \ (resid 369 through 370 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 371 through 383)) selection = (chain 'C' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 14 through 22 or (resid \ 23 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 24 through 36 or (resid 37 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 38 through 47 or (resid 48 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 49 \ through 53 or (resid 54 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 55 through 103 or (resid 104 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 105 through \ 115 or (resid 116 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 117 through 139 or (resid 140 through 141 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 142 th \ rough 169 or (resid 170 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 171 through 182 or (resid 183 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name OD2 or name H \ or name HA )) or (resid 184 through 190 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 191 through 197 or (resid 198 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ or name NH1 or name NH2 or name H or name HA )) or resid 199 thro \ ugh 205 or (resid 206 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 207 through 212 or (resid 213 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 214 through 21 \ 5 or (resid 216 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 217 through 265 or (resid 266 through 269 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 270 thro \ ugh 273 or (resid 274 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 275 through 293 or (resid 294 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 295 through 29 \ 6 or (resid 297 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 298 or (resid 299 through 303 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 304 through 305 or ( \ resid 306 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 307 through 351 or (resid 352 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 353 through 383)) selection = (chain 'D' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 14 through 19 or (resid \ 20 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 21 through 22 or (resid 23 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 24 through 36 or (resid 37 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 38 \ through 43 or (resid 44 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 45 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 55 through 79 \ or (resid 80 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 81 through 115 or (resid 116 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 117 or (resid 118 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 119 through 139 or (resid 140 through 141 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 142 through 155 or (resid 156 \ through 157 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 158 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 171 through 172 or (resi \ d 173 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 174 through 177 or (resid 178 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 179 through 181 or (resid 182 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 183 or (resid 184 through 190 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 191 through 196 or (resid 197 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or (resi \ d 198 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) or resid \ 199 or (resid 200 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 201 through 205 or (resid 206 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 207 through 212 o \ r (resid 213 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 214 through 215 or (resid 216 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 217 through 230 or (res \ id 231 through 232 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 233 or (resid 234 through 236 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 237 through 260 o \ r (resid 261 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 262 through 265 or (resid 266 through 269 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 270 through \ 278 or (resid 279 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 280 through 296 or (resid 297 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 298 or (resid 299 \ through 303 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 304 through 305 or (resid 306 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 307 or (resid 308 throu \ gh 309 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 310 through 324 or (resid 325 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 326 through 330 or (resid 331 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 332 through 333 or (resid 334 through 335 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 336 through 343 or (res \ id 344 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA )) or resid 345 or (resid 346 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 347 th \ rough 351 or (resid 352 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 353 through 361 or (resid 362 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 363 through \ 369 or (resid 370 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 371 through 383)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.160 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.480 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.006 0.066 11626 Z= 0.259 Angle : 1.012 60.024 15887 Z= 0.399 Chirality : 0.066 1.641 1856 Planarity : 0.003 0.040 2039 Dihedral : 11.316 87.331 3855 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.18), residues: 1488 helix: -1.35 (0.18), residues: 596 sheet: -2.44 (0.30), residues: 252 loop : -3.35 (0.19), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 141 TYR 0.013 0.001 TYR D 77 PHE 0.009 0.001 PHE A 36 TRP 0.013 0.001 TRP D 323 HIS 0.007 0.001 HIS D 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (11611) covalent geometry : angle 0.49276 / 0.27 (15846) SS BOND : bond 0.00226 / 0.12 ( 4) SS BOND : angle 0.54781 / 0.34 ( 8) hydrogen bonds : bond 0.11567 / 7.49 ( 539) hydrogen bonds : angle 6.06873 / 4.27 ( 1593) link_BETA1-4 : bond 0.06504 / 3.47 ( 6) link_BETA1-4 : angle 26.20515 / 18.30 ( 18) link_NAG-ASN : bond 0.00322 / 0.18 ( 5) link_NAG-ASN : angle 1.81627 / 1.38 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.495 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: C 339 GLU cc_start: 0.6795 (tp30) cc_final: 0.6577 (tp30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2868 time to fit residues: 46.3484 Evaluate side-chains 63 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 13 GLN C 93 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN A 147 GLN A 246 GLN A 290 GLN A 344 ASN B 112 GLN D 236 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.090752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074783 restraints weight = 78834.740| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.11 r_work: 0.3135 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11626 Z= 0.159 Angle : 0.480 6.568 15887 Z= 0.258 Chirality : 0.041 0.155 1856 Planarity : 0.004 0.049 2039 Dihedral : 3.575 18.217 1598 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.71 % Allowed : 7.02 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.21), residues: 1488 helix: 0.10 (0.20), residues: 604 sheet: -2.11 (0.31), residues: 252 loop : -2.67 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 297 TYR 0.015 0.001 TYR D 77 PHE 0.026 0.001 PHE A 41 TRP 0.010 0.001 TRP D 262 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (11611) covalent geometry : angle 0.47118 / 0.26 (15846) SS BOND : bond 0.00146 / 0.07 ( 4) SS BOND : angle 0.55330 / 0.41 ( 8) hydrogen bonds : bond 0.03718 / 2.45 ( 539) hydrogen bonds : angle 4.73384 / 3.33 ( 1593) link_BETA1-4 : bond 0.01402 / 0.82 ( 6) link_BETA1-4 : angle 2.42003 / 1.84 ( 18) link_NAG-ASN : bond 0.00303 / 0.18 ( 5) link_NAG-ASN : angle 1.41873 / 1.08 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 0.2723 time to fit residues: 27.0394 Evaluate side-chains 67 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain D residue 382 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.091306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075231 restraints weight = 78891.236| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.13 r_work: 0.3144 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11626 Z= 0.101 Angle : 0.419 4.831 15887 Z= 0.228 Chirality : 0.039 0.148 1856 Planarity : 0.003 0.037 2039 Dihedral : 3.429 17.552 1598 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.36 % Allowed : 7.64 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.22), residues: 1488 helix: 0.96 (0.21), residues: 596 sheet: -1.88 (0.32), residues: 252 loop : -2.29 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 68 TYR 0.010 0.001 TYR B 286 PHE 0.016 0.001 PHE A 41 TRP 0.011 0.001 TRP D 262 HIS 0.011 0.001 HIS C 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (11611) covalent geometry : angle 0.41119 / 0.23 (15846) SS BOND : bond 0.00095 / 0.05 ( 4) SS BOND : angle 0.53335 / 0.37 ( 8) hydrogen bonds : bond 0.03304 / 2.19 ( 539) hydrogen bonds : angle 4.41352 / 3.11 ( 1593) link_BETA1-4 : bond 0.00387 / 0.23 ( 6) link_BETA1-4 : angle 2.04351 / 1.39 ( 18) link_NAG-ASN : bond 0.00177 / 0.11 ( 5) link_NAG-ASN : angle 1.44123 / 1.08 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ARG cc_start: 0.7348 (mtm-85) cc_final: 0.7088 (mtm-85) REVERT: B 231 ASP cc_start: 0.7921 (t0) cc_final: 0.7684 (t70) REVERT: B 234 LYS cc_start: 0.8892 (pttt) cc_final: 0.8551 (pttt) outliers start: 4 outliers final: 4 residues processed: 68 average time/residue: 0.2844 time to fit residues: 27.1294 Evaluate side-chains 63 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 378 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070596 restraints weight = 80280.999| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.09 r_work: 0.3049 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 11626 Z= 0.268 Angle : 0.535 8.319 15887 Z= 0.288 Chirality : 0.041 0.154 1856 Planarity : 0.004 0.040 2039 Dihedral : 3.670 19.327 1598 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.71 % Allowed : 8.71 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.22), residues: 1488 helix: 1.04 (0.21), residues: 596 sheet: -1.83 (0.33), residues: 252 loop : -2.27 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 178 TYR 0.017 0.002 TYR D 77 PHE 0.014 0.001 PHE A 41 TRP 0.009 0.001 TRP D 323 HIS 0.006 0.001 HIS C 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.27 (11611) covalent geometry : angle 0.52482 / 0.29 (15846) SS BOND : bond 0.00252 / 0.13 ( 4) SS BOND : angle 0.60141 / 0.47 ( 8) hydrogen bonds : bond 0.03877 / 2.54 ( 539) hydrogen bonds : angle 4.60475 / 3.26 ( 1593) link_BETA1-4 : bond 0.00820 / 0.44 ( 6) link_BETA1-4 : angle 2.52120 / 1.73 ( 18) link_NAG-ASN : bond 0.00640 / 0.38 ( 5) link_NAG-ASN : angle 1.96424 / 1.49 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 ASP cc_start: 0.8222 (t0) cc_final: 0.7879 (t70) outliers start: 8 outliers final: 7 residues processed: 61 average time/residue: 0.2507 time to fit residues: 22.4275 Evaluate side-chains 61 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 378 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071495 restraints weight = 79439.380| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.12 r_work: 0.3060 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11626 Z= 0.165 Angle : 0.454 5.300 15887 Z= 0.245 Chirality : 0.040 0.147 1856 Planarity : 0.003 0.036 2039 Dihedral : 3.571 18.639 1598 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.36 % Allowed : 10.04 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1488 helix: 1.25 (0.21), residues: 608 sheet: -1.77 (0.33), residues: 252 loop : -2.21 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 178 TYR 0.009 0.001 TYR B 77 PHE 0.012 0.001 PHE A 41 TRP 0.009 0.001 TRP D 262 HIS 0.006 0.001 HIS C 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (11611) covalent geometry : angle 0.44629 / 0.24 (15846) SS BOND : bond 0.00181 / 0.09 ( 4) SS BOND : angle 0.55037 / 0.41 ( 8) hydrogen bonds : bond 0.03432 / 2.26 ( 539) hydrogen bonds : angle 4.37966 / 3.09 ( 1593) link_BETA1-4 : bond 0.00422 / 0.22 ( 6) link_BETA1-4 : angle 1.91725 / 1.32 ( 18) link_NAG-ASN : bond 0.00336 / 0.20 ( 5) link_NAG-ASN : angle 1.74723 / 1.30 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 ASP cc_start: 0.8244 (t0) cc_final: 0.7846 (t70) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.2353 time to fit residues: 19.7848 Evaluate side-chains 56 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 378 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 114 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071732 restraints weight = 79990.575| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.11 r_work: 0.3073 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11626 Z= 0.132 Angle : 0.431 4.579 15887 Z= 0.232 Chirality : 0.039 0.143 1856 Planarity : 0.003 0.038 2039 Dihedral : 3.455 18.176 1598 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.53 % Allowed : 10.22 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1488 helix: 1.60 (0.21), residues: 600 sheet: -1.71 (0.33), residues: 252 loop : -1.91 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 68 TYR 0.009 0.001 TYR B 286 PHE 0.012 0.001 PHE A 41 TRP 0.010 0.001 TRP D 262 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11611) covalent geometry : angle 0.42436 / 0.23 (15846) SS BOND : bond 0.00141 / 0.07 ( 4) SS BOND : angle 0.51711 / 0.38 ( 8) hydrogen bonds : bond 0.03216 / 2.12 ( 539) hydrogen bonds : angle 4.20263 / 2.97 ( 1593) link_BETA1-4 : bond 0.00463 / 0.25 ( 6) link_BETA1-4 : angle 1.73035 / 1.20 ( 18) link_NAG-ASN : bond 0.00268 / 0.16 ( 5) link_NAG-ASN : angle 1.65401 / 1.23 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 ASP cc_start: 0.8200 (t0) cc_final: 0.7812 (t70) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.2329 time to fit residues: 20.2555 Evaluate side-chains 58 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain B residue 378 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.071696 restraints weight = 79577.259| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.09 r_work: 0.3069 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11626 Z= 0.135 Angle : 0.427 4.471 15887 Z= 0.230 Chirality : 0.039 0.141 1856 Planarity : 0.003 0.036 2039 Dihedral : 3.420 17.853 1598 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.53 % Allowed : 10.58 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.22), residues: 1488 helix: 1.66 (0.21), residues: 612 sheet: -1.59 (0.33), residues: 252 loop : -1.85 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 178 TYR 0.009 0.001 TYR D 77 PHE 0.011 0.001 PHE A 41 TRP 0.009 0.001 TRP D 262 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11611) covalent geometry : angle 0.42018 / 0.23 (15846) SS BOND : bond 0.00160 / 0.08 ( 4) SS BOND : angle 0.49910 / 0.35 ( 8) hydrogen bonds : bond 0.03154 / 2.08 ( 539) hydrogen bonds : angle 4.11771 / 2.92 ( 1593) link_BETA1-4 : bond 0.00434 / 0.23 ( 6) link_BETA1-4 : angle 1.69091 / 1.17 ( 18) link_NAG-ASN : bond 0.00279 / 0.17 ( 5) link_NAG-ASN : angle 1.64486 / 1.23 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 ASP cc_start: 0.8242 (t0) cc_final: 0.7923 (t70) REVERT: B 362 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8048 (mt-10) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 0.2454 time to fit residues: 22.9806 Evaluate side-chains 59 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 378 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS B 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.070054 restraints weight = 80376.833| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.15 r_work: 0.3029 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11626 Z= 0.221 Angle : 0.481 6.394 15887 Z= 0.260 Chirality : 0.040 0.141 1856 Planarity : 0.003 0.037 2039 Dihedral : 3.595 18.538 1598 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.71 % Allowed : 10.84 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1488 helix: 1.70 (0.21), residues: 588 sheet: -1.62 (0.33), residues: 252 loop : -1.84 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 178 TYR 0.013 0.001 TYR B 77 PHE 0.010 0.001 PHE A 41 TRP 0.009 0.001 TRP D 323 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (11611) covalent geometry : angle 0.47265 / 0.26 (15846) SS BOND : bond 0.00252 / 0.13 ( 4) SS BOND : angle 0.52257 / 0.40 ( 8) hydrogen bonds : bond 0.03493 / 2.28 ( 539) hydrogen bonds : angle 4.30332 / 3.06 ( 1593) link_BETA1-4 : bond 0.00615 / 0.33 ( 6) link_BETA1-4 : angle 2.06674 / 1.41 ( 18) link_NAG-ASN : bond 0.00494 / 0.30 ( 5) link_NAG-ASN : angle 1.86517 / 1.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: B 231 ASP cc_start: 0.8322 (t0) cc_final: 0.7858 (t0) REVERT: B 294 GLU cc_start: 0.8755 (tp30) cc_final: 0.8522 (tp30) REVERT: B 362 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8077 (mt-10) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.2488 time to fit residues: 22.4654 Evaluate side-chains 57 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 378 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 71 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.087194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.070918 restraints weight = 80150.601| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.13 r_work: 0.3048 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11626 Z= 0.147 Angle : 0.445 4.597 15887 Z= 0.239 Chirality : 0.040 0.141 1856 Planarity : 0.003 0.037 2039 Dihedral : 3.542 17.916 1598 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.53 % Allowed : 11.20 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1488 helix: 1.87 (0.21), residues: 588 sheet: -1.58 (0.33), residues: 252 loop : -1.74 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 141 TYR 0.009 0.001 TYR B 77 PHE 0.011 0.001 PHE A 41 TRP 0.009 0.001 TRP D 262 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (11611) covalent geometry : angle 0.43854 / 0.24 (15846) SS BOND : bond 0.00174 / 0.09 ( 4) SS BOND : angle 0.53403 / 0.39 ( 8) hydrogen bonds : bond 0.03260 / 2.15 ( 539) hydrogen bonds : angle 4.18188 / 2.97 ( 1593) link_BETA1-4 : bond 0.00412 / 0.22 ( 6) link_BETA1-4 : angle 1.72206 / 1.18 ( 18) link_NAG-ASN : bond 0.00311 / 0.19 ( 5) link_NAG-ASN : angle 1.73103 / 1.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 GLU cc_start: 0.8772 (tp30) cc_final: 0.8539 (tp30) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.2211 time to fit residues: 19.7449 Evaluate side-chains 57 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 378 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072114 restraints weight = 79852.495| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.10 r_work: 0.3074 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11626 Z= 0.095 Angle : 0.414 3.953 15887 Z= 0.223 Chirality : 0.039 0.139 1856 Planarity : 0.003 0.038 2039 Dihedral : 3.371 17.260 1598 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.36 % Allowed : 11.56 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1488 helix: 2.00 (0.22), residues: 600 sheet: -1.51 (0.33), residues: 252 loop : -1.53 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 141 TYR 0.009 0.001 TYR B 286 PHE 0.010 0.001 PHE A 41 TRP 0.012 0.001 TRP D 262 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (11611) covalent geometry : angle 0.40814 / 0.22 (15846) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.49647 / 0.36 ( 8) hydrogen bonds : bond 0.02962 / 1.96 ( 539) hydrogen bonds : angle 4.00957 / 2.84 ( 1593) link_BETA1-4 : bond 0.00412 / 0.22 ( 6) link_BETA1-4 : angle 1.47091 / 1.02 ( 18) link_NAG-ASN : bond 0.00167 / 0.09 ( 5) link_NAG-ASN : angle 1.56667 / 1.15 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 44 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LEU 232 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue ILE 235 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 213 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue ILE 306 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue SER 37 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 GLU cc_start: 0.8726 (tp30) cc_final: 0.8505 (tp30) outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.2646 time to fit residues: 22.2054 Evaluate side-chains 58 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 378 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 29 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 61 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.088450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071930 restraints weight = 79934.918| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.21 r_work: 0.3070 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11626 Z= 0.096 Angle : 0.412 5.837 15887 Z= 0.222 Chirality : 0.039 0.137 1856 Planarity : 0.003 0.038 2039 Dihedral : 3.297 16.946 1598 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.27 % Allowed : 11.56 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1488 helix: 1.95 (0.22), residues: 624 sheet: -1.46 (0.33), residues: 252 loop : -1.52 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 141 TYR 0.008 0.001 TYR B 286 PHE 0.010 0.001 PHE A 41 TRP 0.011 0.001 TRP D 262 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (11611) covalent geometry : angle 0.40713 / 0.22 (15846) SS BOND : bond 0.00111 / 0.06 ( 4) SS BOND : angle 0.44946 / 0.32 ( 8) hydrogen bonds : bond 0.02911 / 1.93 ( 539) hydrogen bonds : angle 3.94305 / 2.80 ( 1593) link_BETA1-4 : bond 0.00420 / 0.22 ( 6) link_BETA1-4 : angle 1.46926 / 1.03 ( 18) link_NAG-ASN : bond 0.00192 / 0.11 ( 5) link_NAG-ASN : angle 1.54627 / 1.15 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4243.41 seconds wall clock time: 72 minutes 52.66 seconds (4372.66 seconds total)