Starting phenix.real_space_refine on Wed Feb 4 06:47:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lod_63245/02_2026/9lod_63245.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lod_63245/02_2026/9lod_63245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lod_63245/02_2026/9lod_63245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lod_63245/02_2026/9lod_63245.map" model { file = "/net/cci-nas-00/data/ceres_data/9lod_63245/02_2026/9lod_63245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lod_63245/02_2026/9lod_63245.cif" } resolution = 3.16 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5674 2.51 5 N 1502 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8947 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2121 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 244} Chain: "B" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1672 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 191} Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1672 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 191} Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1665 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 190} Chain: "E" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1665 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 190} Chain: "F" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 74 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.26 Number of scatterers: 8947 At special positions: 0 Unit cell: (78.11, 138.03, 101.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1732 8.00 N 1502 7.00 C 5674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 425 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 425 " distance=2.03 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 321 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 425 " 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " BETA1-2 " MAN F 4 " - " NAG F 5 " " MAN G 4 " - " NAG G 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 132 " " NAG F 1 " - " ASN B 297 " " NAG G 1 " - " ASN C 297 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 316.3 milliseconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 34 sheets defined 9.1% alpha, 49.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.708A pdb=" N THR B 359 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.624A pdb=" N GLN B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'C' and resid 309 through 315 removed outlier: 3.637A pdb=" N TRP C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.657A pdb=" N LEU C 358 " --> pdb=" O ARG C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.523A pdb=" N GLN C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 436 removed outlier: 3.518A pdb=" N TYR C 436 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'E' and resid 246 through 252 removed outlier: 3.583A pdb=" N THR E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 251 " --> pdb=" O PRO E 247 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 246 through 252' Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 354 through 359 removed outlier: 4.059A pdb=" N THR E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 432 through 436 removed outlier: 3.542A pdb=" N HIS E 435 " --> pdb=" O LEU E 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 113 through 114 removed outlier: 6.652A pdb=" N VAL A 113 " --> pdb=" O GLN A 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 145 removed outlier: 6.889A pdb=" N ILE A 135 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE A 144 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASN A 133 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASN A 132 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 169 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 140 through 145 removed outlier: 6.889A pdb=" N ILE A 135 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE A 144 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASN A 133 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASN A 132 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 169 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.671A pdb=" N VAL A 193 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 212 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 225 through 229 Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 229 Processing sheet with id=AB2, first strand: chain 'B' and resid 239 through 243 removed outlier: 3.512A pdb=" N SER B 239 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 305 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 274 through 278 removed outlier: 3.601A pdb=" N LYS B 274 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AB5, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.625A pdb=" N PHE B 404 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 347 through 351 removed outlier: 5.625A pdb=" N PHE B 404 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 387 through 388 removed outlier: 4.622A pdb=" N TRP B 381 " --> pdb=" O GLU B 388 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 239 through 243 removed outlier: 3.509A pdb=" N CYS C 261 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 304 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 302 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP C 265 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR C 300 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 243 removed outlier: 3.509A pdb=" N CYS C 261 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 304 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 302 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP C 265 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR C 300 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 282 through 284 removed outlier: 4.242A pdb=" N TRP C 277 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 334 " --> pdb=" O CYS C 321 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 323 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 332 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 347 through 351 removed outlier: 6.106A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 347 through 351 removed outlier: 6.106A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 386 through 388 removed outlier: 4.692A pdb=" N TRP C 381 " --> pdb=" O GLU C 388 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.832A pdb=" N VAL D 259 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP D 265 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TYR D 300 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.832A pdb=" N VAL D 259 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP D 265 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TYR D 300 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 282 through 284 removed outlier: 4.363A pdb=" N TRP D 277 " --> pdb=" O VAL D 284 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 347 through 351 removed outlier: 3.605A pdb=" N LYS D 370 " --> pdb=" O GLN D 347 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 347 through 351 removed outlier: 3.605A pdb=" N LYS D 370 " --> pdb=" O GLN D 347 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N PHE D 404 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 386 through 387 Processing sheet with id=AD2, first strand: chain 'E' and resid 239 through 243 removed outlier: 3.634A pdb=" N THR E 260 " --> pdb=" O PHE E 243 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR E 260 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU E 306 " --> pdb=" O THR E 260 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 262 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER E 304 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL E 264 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL E 302 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 239 through 243 removed outlier: 3.634A pdb=" N THR E 260 " --> pdb=" O PHE E 243 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR E 260 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU E 306 " --> pdb=" O THR E 260 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL E 262 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER E 304 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL E 264 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL E 302 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 282 through 284 removed outlier: 4.559A pdb=" N TRP E 277 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E 336 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 347 through 351 removed outlier: 3.530A pdb=" N LYS E 370 " --> pdb=" O GLN E 347 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 347 through 351 removed outlier: 3.530A pdb=" N LYS E 370 " --> pdb=" O GLN E 347 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LYS E 370 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU E 406 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 386 through 387 383 hydrogen bonds defined for protein. 915 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: 1.71 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2640 1.33 - 1.46: 1786 1.46 - 1.58: 4714 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 9189 Sorted by residual: bond pdb=" CA CYS E 261 " pdb=" CB CYS E 261 " ideal model delta sigma weight residual 1.526 1.564 -0.037 1.53e-02 4.27e+03 5.98e+00 bond pdb=" C ASN B 297 " pdb=" O ASN B 297 " ideal model delta sigma weight residual 1.236 1.216 0.021 1.33e-02 5.65e+03 2.41e+00 bond pdb=" C2 BMA F 3 " pdb=" C3 BMA F 3 " ideal model delta sigma weight residual 1.544 1.514 0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CB GLN D 342 " pdb=" CG GLN D 342 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.10e+00 bond pdb=" CA ASN B 297 " pdb=" C ASN B 297 " ideal model delta sigma weight residual 1.524 1.501 0.024 1.66e-02 3.63e+03 2.06e+00 ... (remaining 9184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 12089 1.35 - 2.70: 311 2.70 - 4.05: 86 4.05 - 5.39: 18 5.39 - 6.74: 7 Bond angle restraints: 12511 Sorted by residual: angle pdb=" CA GLN D 342 " pdb=" CB GLN D 342 " pdb=" CG GLN D 342 " ideal model delta sigma weight residual 114.10 120.64 -6.54 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB GLN D 342 " pdb=" CG GLN D 342 " pdb=" CD GLN D 342 " ideal model delta sigma weight residual 112.60 118.15 -5.55 1.70e+00 3.46e-01 1.07e+01 angle pdb=" C CYS E 261 " pdb=" CA CYS E 261 " pdb=" CB CYS E 261 " ideal model delta sigma weight residual 111.22 115.83 -4.61 1.72e+00 3.38e-01 7.19e+00 angle pdb=" CA CYS E 261 " pdb=" CB CYS E 261 " pdb=" SG CYS E 261 " ideal model delta sigma weight residual 114.40 120.49 -6.09 2.30e+00 1.89e-01 7.02e+00 angle pdb=" N MET A 265 " pdb=" CA MET A 265 " pdb=" C MET A 265 " ideal model delta sigma weight residual 109.81 115.53 -5.72 2.21e+00 2.05e-01 6.69e+00 ... (remaining 12506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 5136 21.29 - 42.57: 522 42.57 - 63.86: 71 63.86 - 85.14: 24 85.14 - 106.43: 6 Dihedral angle restraints: 5759 sinusoidal: 2513 harmonic: 3246 Sorted by residual: dihedral pdb=" CB CYS E 261 " pdb=" SG CYS E 261 " pdb=" SG CYS E 321 " pdb=" CB CYS E 321 " ideal model delta sinusoidal sigma weight residual 93.00 14.29 78.71 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" CB CYS D 261 " pdb=" SG CYS D 261 " pdb=" SG CYS D 321 " pdb=" CB CYS D 321 " ideal model delta sinusoidal sigma weight residual -86.00 -126.33 40.33 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA CYS D 309 " pdb=" C CYS D 309 " pdb=" N HIS D 310 " pdb=" CA HIS D 310 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 5756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 1407 0.153 - 0.306: 0 0.306 - 0.458: 0 0.458 - 0.611: 0 0.611 - 0.764: 1 Chirality restraints: 1408 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 -1.64 -0.76 2.00e-02 2.50e+03 1.46e+03 chirality pdb=" C1 MAN F 4 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 2.26 0.14 2.00e-02 2.50e+03 5.13e+01 chirality pdb=" C1 NAG F 5 " pdb=" O2 MAN F 4 " pdb=" C2 NAG F 5 " pdb=" O5 NAG F 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.52e+01 ... (remaining 1405 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 5 " -0.136 2.00e-02 2.50e+03 1.11e-01 1.53e+02 pdb=" C7 NAG F 5 " 0.042 2.00e-02 2.50e+03 pdb=" C8 NAG F 5 " -0.103 2.00e-02 2.50e+03 pdb=" N2 NAG F 5 " 0.173 2.00e-02 2.50e+03 pdb=" O7 NAG F 5 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.069 2.00e-02 2.50e+03 5.67e-02 4.02e+01 pdb=" C7 NAG F 1 " 0.017 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.051 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.091 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.029 2.00e-02 2.50e+03 2.38e-02 7.09e+00 pdb=" C7 NAG F 2 " -0.008 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.022 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.038 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.006 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 172 2.71 - 3.26: 8231 3.26 - 3.81: 14238 3.81 - 4.35: 17796 4.35 - 4.90: 30608 Nonbonded interactions: 71045 Sorted by model distance: nonbonded pdb=" OD1 ASP D 442 " pdb=" OG SER D 444 " model vdw 2.163 3.040 nonbonded pdb=" O5 NAG F 2 " pdb=" O6 NAG F 2 " model vdw 2.400 2.432 nonbonded pdb=" OH TYR D 407 " pdb=" CG2 THR E 366 " model vdw 2.492 3.460 nonbonded pdb=" O2 BMA F 3 " pdb=" O3 BMA F 3 " model vdw 2.571 2.432 nonbonded pdb=" O2 BMA G 3 " pdb=" O3 BMA G 3 " model vdw 2.579 2.432 ... (remaining 71040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 237 through 444) selection = (chain 'C' and resid 237 through 444) selection = chain 'D' selection = chain 'E' } 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: 5.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.240 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9213 Z= 0.162 Angle : 0.597 6.742 12571 Z= 0.295 Chirality : 0.049 0.764 1408 Planarity : 0.005 0.111 1595 Dihedral : 16.866 106.427 3615 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.79 % Allowed : 21.51 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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 (0.26), residues: 1088 helix: -2.13 (0.52), residues: 70 sheet: -0.34 (0.24), residues: 475 loop : 0.32 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 355 TYR 0.016 0.001 TYR C 436 PHE 0.013 0.001 PHE E 372 TRP 0.018 0.001 TRP A 251 HIS 0.002 0.001 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9189) covalent geometry : angle 0.58335 (12511) SS BOND : bond 0.00301 ( 12) SS BOND : angle 1.61291 ( 24) hydrogen bonds : bond 0.22846 ( 303) hydrogen bonds : angle 10.46304 ( 915) link_ALPHA1-6 : bond 0.00269 ( 2) link_ALPHA1-6 : angle 1.48050 ( 6) link_BETA1-2 : bond 0.00607 ( 2) link_BETA1-2 : angle 1.12236 ( 6) link_BETA1-4 : bond 0.00320 ( 4) link_BETA1-4 : angle 2.80514 ( 12) link_BETA1-6 : bond 0.00634 ( 1) link_BETA1-6 : angle 2.90198 ( 3) link_NAG-ASN : bond 0.00264 ( 3) link_NAG-ASN : angle 1.62063 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: B 300 TYR cc_start: 0.8286 (m-10) cc_final: 0.7671 (m-10) REVERT: C 258 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6223 (pp20) REVERT: D 249 ASP cc_start: 0.7950 (m-30) cc_final: 0.7531 (m-30) REVERT: D 319 TYR cc_start: 0.3925 (m-10) cc_final: 0.3584 (m-10) REVERT: E 380 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7667 (mp0) outliers start: 8 outliers final: 6 residues processed: 145 average time/residue: 0.1002 time to fit residues: 19.8824 Evaluate side-chains 140 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain E residue 380 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN D 325 ASN D 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.176352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137156 restraints weight = 11489.432| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.29 r_work: 0.3315 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9213 Z= 0.146 Angle : 0.561 7.750 12571 Z= 0.283 Chirality : 0.044 0.167 1408 Planarity : 0.004 0.024 1595 Dihedral : 7.077 75.750 1438 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.75 % Allowed : 21.22 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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: -0.15 (0.26), residues: 1088 helix: -2.09 (0.52), residues: 76 sheet: -0.13 (0.24), residues: 470 loop : 0.46 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.010 0.001 TYR D 278 PHE 0.013 0.001 PHE B 372 TRP 0.011 0.001 TRP A 259 HIS 0.002 0.000 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9189) covalent geometry : angle 0.54978 (12511) SS BOND : bond 0.00329 ( 12) SS BOND : angle 1.21560 ( 24) hydrogen bonds : bond 0.04093 ( 303) hydrogen bonds : angle 6.80811 ( 915) link_ALPHA1-6 : bond 0.00455 ( 2) link_ALPHA1-6 : angle 1.65058 ( 6) link_BETA1-2 : bond 0.00953 ( 2) link_BETA1-2 : angle 1.08312 ( 6) link_BETA1-4 : bond 0.00571 ( 4) link_BETA1-4 : angle 2.79599 ( 12) link_BETA1-6 : bond 0.00226 ( 1) link_BETA1-6 : angle 1.71754 ( 3) link_NAG-ASN : bond 0.00096 ( 3) link_NAG-ASN : angle 1.30989 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 275 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8532 (mtp180) REVERT: B 300 TYR cc_start: 0.8222 (m-10) cc_final: 0.8017 (m-10) REVERT: C 318 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6607 (pt0) REVERT: D 246 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6985 (pttt) REVERT: D 249 ASP cc_start: 0.7949 (m-30) cc_final: 0.7622 (m-30) outliers start: 28 outliers final: 16 residues processed: 160 average time/residue: 0.0949 time to fit residues: 21.2922 Evaluate side-chains 145 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 428 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.0030 chunk 99 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN D 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.175048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137698 restraints weight = 11500.935| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.35 r_work: 0.3313 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9213 Z= 0.159 Angle : 0.549 8.127 12571 Z= 0.273 Chirality : 0.044 0.157 1408 Planarity : 0.003 0.026 1595 Dihedral : 6.276 66.408 1428 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.44 % Allowed : 21.02 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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: -0.13 (0.26), residues: 1088 helix: -2.06 (0.50), residues: 82 sheet: -0.05 (0.24), residues: 470 loop : 0.43 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.011 0.001 TYR A 136 PHE 0.012 0.001 PHE B 372 TRP 0.011 0.001 TRP A 251 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9189) covalent geometry : angle 0.53906 (12511) SS BOND : bond 0.00329 ( 12) SS BOND : angle 0.96755 ( 24) hydrogen bonds : bond 0.03480 ( 303) hydrogen bonds : angle 5.93315 ( 915) link_ALPHA1-6 : bond 0.00377 ( 2) link_ALPHA1-6 : angle 1.60653 ( 6) link_BETA1-2 : bond 0.00618 ( 2) link_BETA1-2 : angle 1.18243 ( 6) link_BETA1-4 : bond 0.00537 ( 4) link_BETA1-4 : angle 2.74898 ( 12) link_BETA1-6 : bond 0.00021 ( 1) link_BETA1-6 : angle 1.60134 ( 3) link_NAG-ASN : bond 0.00080 ( 3) link_NAG-ASN : angle 1.24092 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 275 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8510 (mtp180) REVERT: C 288 LYS cc_start: 0.5919 (tttm) cc_final: 0.5437 (mmtt) REVERT: C 318 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6465 (pt0) REVERT: D 249 ASP cc_start: 0.7933 (m-30) cc_final: 0.7369 (m-30) outliers start: 35 outliers final: 22 residues processed: 165 average time/residue: 0.0911 time to fit residues: 21.0973 Evaluate side-chains 156 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 437 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 73 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN B 295 GLN D 276 ASN D 311 GLN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.174274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135478 restraints weight = 11635.377| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.37 r_work: 0.3288 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9213 Z= 0.171 Angle : 0.551 8.022 12571 Z= 0.273 Chirality : 0.044 0.150 1408 Planarity : 0.003 0.026 1595 Dihedral : 5.781 52.907 1427 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.44 % Allowed : 20.92 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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: -0.12 (0.26), residues: 1088 helix: -2.02 (0.50), residues: 82 sheet: -0.10 (0.24), residues: 460 loop : 0.46 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 355 TYR 0.011 0.001 TYR A 136 PHE 0.013 0.001 PHE B 372 TRP 0.010 0.001 TRP A 251 HIS 0.003 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9189) covalent geometry : angle 0.54015 (12511) SS BOND : bond 0.00323 ( 12) SS BOND : angle 0.89770 ( 24) hydrogen bonds : bond 0.03121 ( 303) hydrogen bonds : angle 5.59863 ( 915) link_ALPHA1-6 : bond 0.00304 ( 2) link_ALPHA1-6 : angle 1.63940 ( 6) link_BETA1-2 : bond 0.00535 ( 2) link_BETA1-2 : angle 1.10548 ( 6) link_BETA1-4 : bond 0.00393 ( 4) link_BETA1-4 : angle 2.98883 ( 12) link_BETA1-6 : bond 0.00086 ( 1) link_BETA1-6 : angle 1.62197 ( 3) link_NAG-ASN : bond 0.00060 ( 3) link_NAG-ASN : angle 1.22679 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: C 318 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6377 (pt0) REVERT: C 368 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8350 (tp) REVERT: D 246 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7038 (pttt) REVERT: D 249 ASP cc_start: 0.8029 (m-30) cc_final: 0.7670 (m-30) REVERT: D 319 TYR cc_start: 0.4005 (m-10) cc_final: 0.3800 (m-10) outliers start: 35 outliers final: 26 residues processed: 160 average time/residue: 0.0987 time to fit residues: 21.8620 Evaluate side-chains 154 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 437 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN D 276 ASN D 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.175386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137540 restraints weight = 11523.988| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.31 r_work: 0.3323 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9213 Z= 0.136 Angle : 0.527 7.090 12571 Z= 0.261 Chirality : 0.043 0.145 1408 Planarity : 0.003 0.026 1595 Dihedral : 5.255 45.924 1427 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.65 % Allowed : 22.10 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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: -0.07 (0.26), residues: 1088 helix: -1.98 (0.51), residues: 82 sheet: 0.03 (0.24), residues: 461 loop : 0.41 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 355 TYR 0.010 0.001 TYR A 136 PHE 0.012 0.001 PHE B 372 TRP 0.013 0.001 TRP A 251 HIS 0.002 0.000 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9189) covalent geometry : angle 0.51579 (12511) SS BOND : bond 0.00257 ( 12) SS BOND : angle 0.90869 ( 24) hydrogen bonds : bond 0.02971 ( 303) hydrogen bonds : angle 5.31127 ( 915) link_ALPHA1-6 : bond 0.00360 ( 2) link_ALPHA1-6 : angle 1.60902 ( 6) link_BETA1-2 : bond 0.00561 ( 2) link_BETA1-2 : angle 1.14565 ( 6) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 2.89726 ( 12) link_BETA1-6 : bond 0.00135 ( 1) link_BETA1-6 : angle 1.50818 ( 3) link_NAG-ASN : bond 0.00097 ( 3) link_NAG-ASN : angle 1.14108 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: C 318 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6251 (pt0) REVERT: D 249 ASP cc_start: 0.8016 (m-30) cc_final: 0.7492 (m-30) REVERT: D 277 TRP cc_start: 0.5053 (m100) cc_final: 0.4691 (m100) outliers start: 27 outliers final: 21 residues processed: 158 average time/residue: 0.0850 time to fit residues: 19.0564 Evaluate side-chains 151 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 437 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN ** D 362 GLN ** 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 = 0.4047 r_free = 0.4047 target = 0.173654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136698 restraints weight = 11525.419| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.50 r_work: 0.3282 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.005 0.047 9213 Z= 0.199 Angle : 0.569 6.545 12571 Z= 0.281 Chirality : 0.045 0.215 1408 Planarity : 0.003 0.031 1595 Dihedral : 5.122 44.434 1425 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.63 % Allowed : 21.02 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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: -0.13 (0.26), residues: 1088 helix: -2.06 (0.50), residues: 82 sheet: -0.06 (0.24), residues: 460 loop : 0.41 (0.29), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 355 TYR 0.012 0.001 TYR B 407 PHE 0.014 0.001 PHE B 372 TRP 0.012 0.002 TRP A 251 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 9189) covalent geometry : angle 0.55856 (12511) SS BOND : bond 0.00372 ( 12) SS BOND : angle 0.97535 ( 24) hydrogen bonds : bond 0.03053 ( 303) hydrogen bonds : angle 5.36431 ( 915) link_ALPHA1-6 : bond 0.00224 ( 2) link_ALPHA1-6 : angle 1.71391 ( 6) link_BETA1-2 : bond 0.00443 ( 2) link_BETA1-2 : angle 1.01233 ( 6) link_BETA1-4 : bond 0.00326 ( 4) link_BETA1-4 : angle 2.73773 ( 12) link_BETA1-6 : bond 0.00010 ( 1) link_BETA1-6 : angle 1.69317 ( 3) link_NAG-ASN : bond 0.00100 ( 3) link_NAG-ASN : angle 1.29609 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: C 318 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6328 (pt0) REVERT: C 368 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8454 (tp) REVERT: D 246 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6886 (pttt) REVERT: D 249 ASP cc_start: 0.8233 (m-30) cc_final: 0.7795 (m-30) REVERT: D 277 TRP cc_start: 0.5281 (m100) cc_final: 0.4916 (m100) REVERT: E 312 ASP cc_start: 0.7644 (m-30) cc_final: 0.7251 (t0) outliers start: 37 outliers final: 26 residues processed: 167 average time/residue: 0.0939 time to fit residues: 22.2082 Evaluate side-chains 155 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 400 SER Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 437 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 18 optimal weight: 0.0000 chunk 32 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN B 384 ASN D 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137550 restraints weight = 11615.902| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.45 r_work: 0.3316 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9213 Z= 0.134 Angle : 0.532 6.110 12571 Z= 0.264 Chirality : 0.043 0.172 1408 Planarity : 0.003 0.031 1595 Dihedral : 4.960 43.044 1425 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.34 % Allowed : 21.32 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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 (0.26), residues: 1088 helix: -2.03 (0.51), residues: 82 sheet: 0.04 (0.24), residues: 461 loop : 0.35 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 355 TYR 0.010 0.001 TYR E 407 PHE 0.013 0.001 PHE B 372 TRP 0.013 0.001 TRP A 251 HIS 0.002 0.000 HIS D 310 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9189) covalent geometry : angle 0.52347 (12511) SS BOND : bond 0.00341 ( 12) SS BOND : angle 0.92548 ( 24) hydrogen bonds : bond 0.02917 ( 303) hydrogen bonds : angle 5.18086 ( 915) link_ALPHA1-6 : bond 0.00371 ( 2) link_ALPHA1-6 : angle 1.59830 ( 6) link_BETA1-2 : bond 0.00573 ( 2) link_BETA1-2 : angle 1.11385 ( 6) link_BETA1-4 : bond 0.00366 ( 4) link_BETA1-4 : angle 2.30374 ( 12) link_BETA1-6 : bond 0.00149 ( 1) link_BETA1-6 : angle 1.51089 ( 3) link_NAG-ASN : bond 0.00131 ( 3) link_NAG-ASN : angle 1.14296 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: C 318 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6254 (pt0) REVERT: C 338 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8463 (tttp) REVERT: C 368 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8275 (tp) REVERT: C 430 GLU cc_start: 0.8609 (pt0) cc_final: 0.8209 (pt0) REVERT: D 246 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6965 (pttt) REVERT: D 249 ASP cc_start: 0.8041 (m-30) cc_final: 0.7625 (m-30) REVERT: D 277 TRP cc_start: 0.5300 (m100) cc_final: 0.4973 (m100) REVERT: E 312 ASP cc_start: 0.7441 (m-30) cc_final: 0.7198 (t0) outliers start: 34 outliers final: 25 residues processed: 166 average time/residue: 0.0960 time to fit residues: 22.4983 Evaluate side-chains 158 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 437 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN D 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137970 restraints weight = 11491.112| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.34 r_work: 0.3313 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9213 Z= 0.128 Angle : 0.520 6.091 12571 Z= 0.260 Chirality : 0.043 0.160 1408 Planarity : 0.003 0.033 1595 Dihedral : 4.817 41.488 1425 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.05 % Allowed : 22.00 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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: -0.06 (0.26), residues: 1088 helix: -2.05 (0.50), residues: 82 sheet: 0.08 (0.24), residues: 461 loop : 0.38 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 355 TYR 0.010 0.001 TYR D 373 PHE 0.013 0.001 PHE B 372 TRP 0.012 0.001 TRP A 251 HIS 0.002 0.000 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9189) covalent geometry : angle 0.51375 (12511) SS BOND : bond 0.00249 ( 12) SS BOND : angle 0.83930 ( 24) hydrogen bonds : bond 0.02839 ( 303) hydrogen bonds : angle 5.01961 ( 915) link_ALPHA1-6 : bond 0.00351 ( 2) link_ALPHA1-6 : angle 1.59595 ( 6) link_BETA1-2 : bond 0.00566 ( 2) link_BETA1-2 : angle 1.07344 ( 6) link_BETA1-4 : bond 0.00392 ( 4) link_BETA1-4 : angle 1.95034 ( 12) link_BETA1-6 : bond 0.00171 ( 1) link_BETA1-6 : angle 1.46123 ( 3) link_NAG-ASN : bond 0.00113 ( 3) link_NAG-ASN : angle 1.09722 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 SER cc_start: 0.8678 (t) cc_final: 0.8253 (m) REVERT: C 318 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6219 (pt0) REVERT: C 338 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8485 (tttp) REVERT: C 368 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8264 (tp) REVERT: D 246 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6935 (pttt) REVERT: D 249 ASP cc_start: 0.8027 (m-30) cc_final: 0.7514 (m-30) REVERT: D 255 ARG cc_start: 0.6718 (mtt180) cc_final: 0.6371 (mtt180) REVERT: D 277 TRP cc_start: 0.5344 (m100) cc_final: 0.5012 (m100) REVERT: E 310 HIS cc_start: 0.7864 (m90) cc_final: 0.7609 (m90) REVERT: E 312 ASP cc_start: 0.7403 (m-30) cc_final: 0.7176 (t0) REVERT: E 441 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8098 (pt) outliers start: 31 outliers final: 21 residues processed: 169 average time/residue: 0.1011 time to fit residues: 23.5894 Evaluate side-chains 158 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 0.0000 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN D 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.176095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138302 restraints weight = 11450.972| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.41 r_work: 0.3335 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9213 Z= 0.127 Angle : 0.524 6.151 12571 Z= 0.261 Chirality : 0.043 0.174 1408 Planarity : 0.003 0.035 1595 Dihedral : 4.558 29.007 1420 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.75 % Allowed : 22.30 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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: -0.04 (0.26), residues: 1088 helix: -2.00 (0.51), residues: 82 sheet: 0.11 (0.24), residues: 461 loop : 0.37 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 355 TYR 0.009 0.001 TYR A 136 PHE 0.012 0.001 PHE B 372 TRP 0.013 0.001 TRP A 251 HIS 0.002 0.000 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9189) covalent geometry : angle 0.51792 (12511) SS BOND : bond 0.00244 ( 12) SS BOND : angle 0.84496 ( 24) hydrogen bonds : bond 0.02807 ( 303) hydrogen bonds : angle 4.95657 ( 915) link_ALPHA1-6 : bond 0.00344 ( 2) link_ALPHA1-6 : angle 1.55999 ( 6) link_BETA1-2 : bond 0.00564 ( 2) link_BETA1-2 : angle 1.07990 ( 6) link_BETA1-4 : bond 0.00395 ( 4) link_BETA1-4 : angle 1.83988 ( 12) link_BETA1-6 : bond 0.00183 ( 1) link_BETA1-6 : angle 1.43167 ( 3) link_NAG-ASN : bond 0.00104 ( 3) link_NAG-ASN : angle 1.09147 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 198 SER cc_start: 0.8655 (t) cc_final: 0.8223 (m) REVERT: C 318 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6204 (pt0) REVERT: C 338 LYS cc_start: 0.8753 (ttpt) cc_final: 0.8300 (tttm) REVERT: C 368 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8231 (tp) REVERT: D 246 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6937 (pttt) REVERT: D 249 ASP cc_start: 0.8002 (m-30) cc_final: 0.7498 (m-30) REVERT: D 255 ARG cc_start: 0.6712 (mtt180) cc_final: 0.6385 (mtt180) REVERT: D 277 TRP cc_start: 0.5318 (m100) cc_final: 0.4981 (m100) REVERT: E 310 HIS cc_start: 0.7811 (m90) cc_final: 0.7561 (m90) outliers start: 28 outliers final: 25 residues processed: 162 average time/residue: 0.0982 time to fit residues: 22.1959 Evaluate side-chains 161 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 437 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 51 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN C 386 GLN D 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138529 restraints weight = 11491.686| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.15 r_work: 0.3337 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9213 Z= 0.137 Angle : 0.531 6.164 12571 Z= 0.265 Chirality : 0.043 0.189 1408 Planarity : 0.003 0.037 1595 Dihedral : 4.551 29.276 1420 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.65 % Allowed : 22.59 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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: -0.04 (0.26), residues: 1088 helix: -1.97 (0.51), residues: 82 sheet: 0.12 (0.24), residues: 461 loop : 0.35 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 355 TYR 0.009 0.001 TYR E 407 PHE 0.012 0.001 PHE B 372 TRP 0.041 0.001 TRP B 277 HIS 0.002 0.000 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9189) covalent geometry : angle 0.52535 (12511) SS BOND : bond 0.00275 ( 12) SS BOND : angle 0.81749 ( 24) hydrogen bonds : bond 0.02813 ( 303) hydrogen bonds : angle 4.94082 ( 915) link_ALPHA1-6 : bond 0.00336 ( 2) link_ALPHA1-6 : angle 1.57942 ( 6) link_BETA1-2 : bond 0.00555 ( 2) link_BETA1-2 : angle 1.05774 ( 6) link_BETA1-4 : bond 0.00381 ( 4) link_BETA1-4 : angle 1.80421 ( 12) link_BETA1-6 : bond 0.00160 ( 1) link_BETA1-6 : angle 1.44950 ( 3) link_NAG-ASN : bond 0.00091 ( 3) link_NAG-ASN : angle 1.11247 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 SER cc_start: 0.8759 (t) cc_final: 0.8310 (m) REVERT: C 318 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6244 (pt0) REVERT: C 368 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8394 (tp) REVERT: D 246 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6990 (pttt) REVERT: D 249 ASP cc_start: 0.8158 (m-30) cc_final: 0.7638 (m-30) REVERT: D 255 ARG cc_start: 0.6833 (mtt180) cc_final: 0.6430 (mtt180) REVERT: D 277 TRP cc_start: 0.5427 (m100) cc_final: 0.5082 (m100) REVERT: E 310 HIS cc_start: 0.7882 (m90) cc_final: 0.7635 (m90) outliers start: 27 outliers final: 23 residues processed: 159 average time/residue: 0.1031 time to fit residues: 22.8802 Evaluate side-chains 157 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 437 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.0050 chunk 95 optimal weight: 8.9990 chunk 80 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN C 386 GLN D 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.176290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138814 restraints weight = 11411.563| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.19 r_work: 0.3336 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9213 Z= 0.134 Angle : 0.532 6.089 12571 Z= 0.265 Chirality : 0.043 0.185 1408 Planarity : 0.003 0.037 1595 Dihedral : 4.576 30.256 1420 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.05 % Allowed : 22.59 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.75 % 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 (0.26), residues: 1088 helix: -2.00 (0.50), residues: 82 sheet: 0.13 (0.24), residues: 461 loop : 0.34 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 355 TYR 0.011 0.001 TYR E 407 PHE 0.012 0.001 PHE B 372 TRP 0.042 0.001 TRP B 277 HIS 0.003 0.000 HIS E 310 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9189) covalent geometry : angle 0.52621 (12511) SS BOND : bond 0.00296 ( 12) SS BOND : angle 0.84762 ( 24) hydrogen bonds : bond 0.02803 ( 303) hydrogen bonds : angle 4.92925 ( 915) link_ALPHA1-6 : bond 0.00345 ( 2) link_ALPHA1-6 : angle 1.56910 ( 6) link_BETA1-2 : bond 0.00572 ( 2) link_BETA1-2 : angle 1.07130 ( 6) link_BETA1-4 : bond 0.00388 ( 4) link_BETA1-4 : angle 1.77487 ( 12) link_BETA1-6 : bond 0.00171 ( 1) link_BETA1-6 : angle 1.43660 ( 3) link_NAG-ASN : bond 0.00095 ( 3) link_NAG-ASN : angle 1.10773 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2378.36 seconds wall clock time: 41 minutes 39.77 seconds (2499.77 seconds total)