Starting phenix.real_space_refine on Wed Aug 5 23:33:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r3s_53558/08_2026/9r3s_53558_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r3s_53558/08_2026/9r3s_53558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r3s_53558/08_2026/9r3s_53558_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r3s_53558/08_2026/9r3s_53558_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r3s_53558/08_2026/9r3s_53558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r3s_53558/08_2026/9r3s_53558.map" } resolution = 3.06 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= 0.020 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: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 3774 2.51 5 N 1016 2.21 5 O 1168 1.98 5 H 5670 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11673 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5250 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 5323 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 332, 5290 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 309} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 332, 5290 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 309} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 5318 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 869 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.20, per 1000 atoms: 0.27 Number of scatterers: 11673 At special positions: 0 Unit cell: (66.96, 95.04, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 1168 8.00 N 1016 7.00 C 3774 6.00 H 5670 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS C1359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS A 223 " distance=2.04 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 356 " distance=2.02 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 389 " distance=2.04 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS A 355 " distance=2.04 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS C1384 " distance=2.04 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 294 " distance=2.02 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 389 " distance=2.03 Simple disulfide: pdb=" SG CYS C1349 " - pdb=" SG CYS C1372 " distance=2.03 Simple disulfide: pdb=" SG CYS C1373 " - pdb=" SG CYS C1389 " distance=2.03 Simple disulfide: pdb=" SG CYS C1374 " - pdb=" SG CYS C1401 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG G 1 " - " FUC G 4 " NAG-ASN " NAG C1801 " - " ASN C1366 " " NAG D 1 " - " ASN B 136 " " NAG E 1 " - " ASN B 82 " " NAG F 1 " - " ASN A 136 " " NAG G 1 " - " ASN A 82 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 485.9 milliseconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 10 sheets defined 22.1% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 39 through 57 removed outlier: 3.502A pdb=" N ARG B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.902A pdb=" N TYR B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 104' Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.889A pdb=" N GLN B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 347 Processing helix chain 'A' and resid 37 through 57 removed outlier: 3.751A pdb=" N VAL A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.516A pdb=" N LYS A 123 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 281 through 287 removed outlier: 3.801A pdb=" N CYS A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.787A pdb=" N ALA A 341 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 1368 through 1373 Processing helix chain 'C' and resid 1394 through 1401 Processing sheet with id=AA1, first strand: chain 'B' and resid 194 through 199 removed outlier: 3.675A pdb=" N GLU B 154 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 106 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL A 376 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N ARG B 110 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 381 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU A 362 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR A 369 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE A 311 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 130 through 136 removed outlier: 3.685A pdb=" N GLU B 215 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY B 216 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 166 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 186 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 168 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN B 184 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 170 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 313 removed outlier: 7.118A pdb=" N ILE B 311 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR B 369 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 313 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N CYS B 356 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N CYS B 387 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG B 385 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 360 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 383 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B 362 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 381 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N ARG A 110 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B 376 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 313 removed outlier: 7.118A pdb=" N ILE B 311 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR B 369 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 313 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N CYS B 356 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N CYS B 387 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG B 385 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 360 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 383 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU B 362 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 381 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N ARG A 110 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL B 376 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A 235 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 329 removed outlier: 6.026A pdb=" N TYR B 328 " --> pdb=" O ILE C1386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 136 removed outlier: 5.118A pdb=" N GLY A 216 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 168 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN A 184 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 170 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 294 through 296 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'C' and resid 1348 through 1349 205 hydrogen bonds defined for protein. 567 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: 2.63 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 5670 1.04 - 1.24: 788 1.24 - 1.44: 1826 1.44 - 1.64: 3429 1.64 - 1.85: 58 Bond restraints: 11771 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 11766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 20188 1.26 - 2.53: 890 2.53 - 3.79: 92 3.79 - 5.06: 26 5.06 - 6.32: 15 Bond angle restraints: 21211 Sorted by residual: angle pdb=" N VAL C1378 " pdb=" CA VAL C1378 " pdb=" C VAL C1378 " ideal model delta sigma weight residual 112.96 109.01 3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" CA CYS B 33 " pdb=" CB CYS B 33 " pdb=" SG CYS B 33 " ideal model delta sigma weight residual 114.40 108.81 5.59 2.30e+00 1.89e-01 5.92e+00 angle pdb=" N ILE A 329 " pdb=" CA ILE A 329 " pdb=" C ILE A 329 " ideal model delta sigma weight residual 112.29 110.14 2.15 9.40e-01 1.13e+00 5.23e+00 angle pdb=" C GLU A 215 " pdb=" N GLY A 216 " pdb=" CA GLY A 216 " ideal model delta sigma weight residual 121.15 117.28 3.87 1.80e+00 3.09e-01 4.62e+00 angle pdb=" CA VAL C1378 " pdb=" C VAL C1378 " pdb=" N GLY C1379 " ideal model delta sigma weight residual 118.65 116.36 2.29 1.07e+00 8.73e-01 4.59e+00 ... (remaining 21206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.28: 5280 22.28 - 44.56: 388 44.56 - 66.84: 108 66.84 - 89.12: 33 89.12 - 111.41: 16 Dihedral angle restraints: 5825 sinusoidal: 3323 harmonic: 2502 Sorted by residual: dihedral pdb=" CB CYS B 223 " pdb=" SG CYS B 223 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -172.11 86.11 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS C1374 " pdb=" SG CYS C1374 " pdb=" SG CYS C1401 " pdb=" CB CYS C1401 " ideal model delta sinusoidal sigma weight residual -86.00 -146.58 60.58 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS B 225 " pdb=" SG CYS B 225 " pdb=" SG CYS A 223 " pdb=" CB CYS A 223 " ideal model delta sinusoidal sigma weight residual 93.00 39.15 53.85 1 1.00e+01 1.00e-02 3.94e+01 ... (remaining 5822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 799 0.055 - 0.110: 115 0.110 - 0.164: 28 0.164 - 0.219: 1 0.219 - 0.274: 4 Chirality restraints: 947 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.51e+00 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.86e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 944 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1364 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C1365 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C1365 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C1365 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 192 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 193 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 364 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO B 365 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " 0.016 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 618 2.16 - 2.77: 22515 2.77 - 3.38: 32325 3.38 - 3.99: 43208 3.99 - 4.60: 66136 Nonbonded interactions: 164802 Sorted by model distance: nonbonded pdb=" OE2 GLU B 362 " pdb="HH11 ARG B 385 " model vdw 1.556 2.450 nonbonded pdb="HH21 ARG B 110 " pdb=" OG SER A 83 " model vdw 1.586 2.450 nonbonded pdb=" O CYS A 355 " pdb=" H SER A 390 " model vdw 1.601 2.450 nonbonded pdb="HH21 ARG B 152 " pdb=" OE2 GLU B 154 " model vdw 1.616 2.450 nonbonded pdb="HD22 ASN B 320 " pdb=" O VAL B 384 " model vdw 1.626 2.450 ... (remaining 164797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 90 or resid 99 through 122 or resid 124 through \ 239 or (resid 252 and (name N or name CA or name C or name O or name HA2 or nam \ e HA3)) or resid 253 through 269 or (resid 283 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2)) or resid 284 through 3 \ 11 or resid 313 through 390)) selection = (chain 'B' and (resid 33 through 122 or resid 124 through 311 or resid 313 throu \ gh 333 or (resid 334 through 335 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 336 through 390)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.36 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: 1.240 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: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.830 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 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 0.039 6132 Z= 0.203 Angle : 0.723 7.683 8349 Z= 0.337 Chirality : 0.046 0.274 947 Planarity : 0.005 0.055 1040 Dihedral : 19.531 111.405 2526 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 0.94 % Allowed : 18.94 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.31), residues: 707 helix: 0.45 (0.46), residues: 139 sheet: -1.00 (0.36), residues: 180 loop : -1.44 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 110 TYR 0.010 0.001 TYR B 328 PHE 0.010 0.001 PHE B 198 TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 6101) covalent geometry : angle 0.69463 / 0.33 ( 8272) SS BOND : bond 0.00556 / 0.33 ( 16) SS BOND : angle 1.49350 / 0.90 ( 32) hydrogen bonds : bond 0.14722 / 9.25 ( 181) hydrogen bonds : angle 7.95761 / 5.93 ( 567) link_BETA1-4 : bond 0.00486 / 0.24 ( 8) link_BETA1-4 : angle 2.57268 / 1.33 ( 24) link_BETA1-6 : bond 0.00334 / 0.17 ( 2) link_BETA1-6 : angle 1.63441 / 0.69 ( 6) link_NAG-ASN : bond 0.00598 / 0.31 ( 5) link_NAG-ASN : angle 2.87152 / 1.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: C 1348 GLU cc_start: 0.6881 (pt0) cc_final: 0.6578 (pt0) REVERT: C 1383 ASN cc_start: 0.7324 (p0) cc_final: 0.6760 (m-40) outliers start: 6 outliers final: 2 residues processed: 86 average time/residue: 0.1863 time to fit residues: 21.3058 Evaluate side-chains 79 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN C1361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.170755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142167 restraints weight = 28443.882| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.72 r_work: 0.3558 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6132 Z= 0.139 Angle : 0.644 5.900 8349 Z= 0.308 Chirality : 0.042 0.150 947 Planarity : 0.005 0.053 1040 Dihedral : 12.395 65.518 1102 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 1.41 % Allowed : 20.66 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.31), residues: 707 helix: 0.36 (0.45), residues: 140 sheet: -1.28 (0.35), residues: 189 loop : -1.16 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 180 TYR 0.009 0.001 TYR C1351 PHE 0.007 0.001 PHE B 198 TRP 0.006 0.001 TRP A 310 HIS 0.002 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6101) covalent geometry : angle 0.61519 / 0.30 ( 8272) SS BOND : bond 0.00340 / 0.25 ( 16) SS BOND : angle 1.25516 / 0.75 ( 32) hydrogen bonds : bond 0.04383 / 2.86 ( 181) hydrogen bonds : angle 6.28375 / 4.58 ( 567) link_BETA1-4 : bond 0.00645 / 0.31 ( 8) link_BETA1-4 : angle 2.85314 / 1.51 ( 24) link_BETA1-6 : bond 0.00373 / 0.19 ( 2) link_BETA1-6 : angle 1.41183 / 0.57 ( 6) link_NAG-ASN : bond 0.00622 / 0.32 ( 5) link_NAG-ASN : angle 2.29205 / 1.08 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.316 Fit side-chains REVERT: A 382 MET cc_start: 0.9025 (mmm) cc_final: 0.8651 (mmm) REVERT: C 1383 ASN cc_start: 0.7467 (p0) cc_final: 0.7035 (m-40) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.2028 time to fit residues: 22.5673 Evaluate side-chains 83 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 1361 ASN Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN C1361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140043 restraints weight = 30088.149| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.81 r_work: 0.3540 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6132 Z= 0.175 Angle : 0.639 5.847 8349 Z= 0.310 Chirality : 0.042 0.153 947 Planarity : 0.005 0.049 1040 Dihedral : 8.943 58.840 1102 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 1.56 % Allowed : 20.19 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.31), residues: 707 helix: 0.31 (0.45), residues: 140 sheet: -1.27 (0.35), residues: 190 loop : -1.24 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 152 TYR 0.013 0.001 TYR C1350 PHE 0.009 0.001 PHE B 198 TRP 0.008 0.001 TRP A 310 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 6101) covalent geometry : angle 0.61214 / 0.30 ( 8272) SS BOND : bond 0.00389 / 0.27 ( 16) SS BOND : angle 1.25012 / 0.72 ( 32) hydrogen bonds : bond 0.04247 / 2.75 ( 181) hydrogen bonds : angle 6.07863 / 4.42 ( 567) link_BETA1-4 : bond 0.00447 / 0.22 ( 8) link_BETA1-4 : angle 2.69184 / 1.42 ( 24) link_BETA1-6 : bond 0.00504 / 0.27 ( 2) link_BETA1-6 : angle 1.46928 / 0.62 ( 6) link_NAG-ASN : bond 0.00568 / 0.29 ( 5) link_NAG-ASN : angle 2.25602 / 1.09 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.310 Fit side-chains REVERT: A 161 LYS cc_start: 0.8340 (ptpt) cc_final: 0.7667 (pttp) REVERT: A 206 GLN cc_start: 0.7842 (tt0) cc_final: 0.7540 (mt0) REVERT: A 382 MET cc_start: 0.9028 (mmm) cc_final: 0.8680 (mmm) REVERT: C 1361 ASN cc_start: 0.6568 (OUTLIER) cc_final: 0.6348 (m110) REVERT: C 1383 ASN cc_start: 0.7411 (p0) cc_final: 0.7002 (m-40) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.1620 time to fit residues: 18.0565 Evaluate side-chains 82 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 1361 ASN Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.170091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.141737 restraints weight = 28033.851| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.70 r_work: 0.3556 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6132 Z= 0.142 Angle : 0.602 5.244 8349 Z= 0.295 Chirality : 0.041 0.152 947 Planarity : 0.004 0.055 1040 Dihedral : 7.104 58.615 1102 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 1.72 % Allowed : 19.72 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.31), residues: 707 helix: 0.35 (0.45), residues: 140 sheet: -1.21 (0.35), residues: 189 loop : -1.21 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 152 TYR 0.008 0.001 TYR B 368 PHE 0.008 0.001 PHE B 124 TRP 0.006 0.001 TRP A 310 HIS 0.002 0.001 HIS B 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6101) covalent geometry : angle 0.57728 / 0.29 ( 8272) SS BOND : bond 0.00309 / 0.22 ( 16) SS BOND : angle 1.09444 / 0.62 ( 32) hydrogen bonds : bond 0.03916 / 2.54 ( 181) hydrogen bonds : angle 5.92754 / 4.30 ( 567) link_BETA1-4 : bond 0.00537 / 0.28 ( 8) link_BETA1-4 : angle 2.48370 / 1.32 ( 24) link_BETA1-6 : bond 0.00307 / 0.16 ( 2) link_BETA1-6 : angle 1.30405 / 0.55 ( 6) link_NAG-ASN : bond 0.00537 / 0.27 ( 5) link_NAG-ASN : angle 2.12528 / 1.02 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8334 (ptpt) cc_final: 0.7651 (pttp) REVERT: A 206 GLN cc_start: 0.7792 (tt0) cc_final: 0.7515 (mt0) REVERT: A 230 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.6995 (m110) REVERT: A 382 MET cc_start: 0.8993 (mmm) cc_final: 0.8644 (mmm) REVERT: C 1383 ASN cc_start: 0.7464 (p0) cc_final: 0.7115 (m-40) outliers start: 11 outliers final: 8 residues processed: 86 average time/residue: 0.2038 time to fit residues: 22.9676 Evaluate side-chains 87 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.0470 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144172 restraints weight = 28099.153| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.76 r_work: 0.3557 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6132 Z= 0.128 Angle : 0.582 4.955 8349 Z= 0.287 Chirality : 0.041 0.203 947 Planarity : 0.004 0.057 1040 Dihedral : 6.298 58.260 1102 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 1.56 % Allowed : 20.34 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.31), residues: 707 helix: 0.39 (0.45), residues: 145 sheet: -1.14 (0.36), residues: 189 loop : -1.21 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 185 TYR 0.009 0.001 TYR B 368 PHE 0.007 0.001 PHE B 124 TRP 0.006 0.001 TRP A 310 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6101) covalent geometry : angle 0.56068 / 0.28 ( 8272) SS BOND : bond 0.00287 / 0.20 ( 16) SS BOND : angle 1.02582 / 0.57 ( 32) hydrogen bonds : bond 0.03769 / 2.45 ( 181) hydrogen bonds : angle 5.82829 / 4.22 ( 567) link_BETA1-4 : bond 0.00446 / 0.22 ( 8) link_BETA1-4 : angle 2.22066 / 1.17 ( 24) link_BETA1-6 : bond 0.00391 / 0.20 ( 2) link_BETA1-6 : angle 1.30950 / 0.54 ( 6) link_NAG-ASN : bond 0.00522 / 0.26 ( 5) link_NAG-ASN : angle 2.04672 / 0.99 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8325 (ptpt) cc_final: 0.7675 (pttp) REVERT: A 206 GLN cc_start: 0.7791 (tt0) cc_final: 0.7532 (mt0) REVERT: A 213 GLU cc_start: 0.7004 (tp30) cc_final: 0.6796 (tm-30) REVERT: A 230 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.6968 (m110) REVERT: A 382 MET cc_start: 0.9011 (mmm) cc_final: 0.8679 (mmm) REVERT: C 1361 ASN cc_start: 0.6069 (m-40) cc_final: 0.5278 (m-40) REVERT: C 1383 ASN cc_start: 0.7463 (p0) cc_final: 0.7093 (m-40) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.2017 time to fit residues: 22.5875 Evaluate side-chains 88 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.0570 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.162267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135685 restraints weight = 26964.525| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.43 r_work: 0.3444 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6132 Z= 0.132 Angle : 0.575 4.938 8349 Z= 0.284 Chirality : 0.040 0.151 947 Planarity : 0.004 0.058 1040 Dihedral : 5.882 58.118 1102 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 1.72 % Allowed : 20.81 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.31), residues: 707 helix: 0.43 (0.45), residues: 144 sheet: -1.13 (0.36), residues: 189 loop : -1.20 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.008 0.001 TYR B 368 PHE 0.008 0.001 PHE B 124 TRP 0.006 0.001 TRP A 310 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6101) covalent geometry : angle 0.55577 / 0.28 ( 8272) SS BOND : bond 0.00304 / 0.20 ( 16) SS BOND : angle 1.04953 / 0.59 ( 32) hydrogen bonds : bond 0.03740 / 2.43 ( 181) hydrogen bonds : angle 5.78141 / 4.19 ( 567) link_BETA1-4 : bond 0.00419 / 0.20 ( 8) link_BETA1-4 : angle 2.03498 / 1.07 ( 24) link_BETA1-6 : bond 0.00393 / 0.21 ( 2) link_BETA1-6 : angle 1.27720 / 0.53 ( 6) link_NAG-ASN : bond 0.00509 / 0.26 ( 5) link_NAG-ASN : angle 2.02591 / 0.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8378 (ptpt) cc_final: 0.7699 (pttp) REVERT: A 206 GLN cc_start: 0.7879 (tt0) cc_final: 0.7489 (mt0) REVERT: A 213 GLU cc_start: 0.7297 (tp30) cc_final: 0.6827 (tm-30) REVERT: A 230 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7050 (m110) REVERT: A 382 MET cc_start: 0.9008 (mmm) cc_final: 0.8684 (mmm) REVERT: C 1361 ASN cc_start: 0.6161 (m-40) cc_final: 0.5356 (m-40) REVERT: C 1383 ASN cc_start: 0.7544 (p0) cc_final: 0.7059 (m-40) outliers start: 11 outliers final: 9 residues processed: 83 average time/residue: 0.2130 time to fit residues: 22.9995 Evaluate side-chains 86 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.161222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136453 restraints weight = 22669.186| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.18 r_work: 0.3470 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6132 Z= 0.125 Angle : 0.567 4.817 8349 Z= 0.281 Chirality : 0.040 0.151 947 Planarity : 0.004 0.060 1040 Dihedral : 5.742 57.987 1102 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 1.72 % Allowed : 20.81 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.31), residues: 707 helix: 0.44 (0.45), residues: 144 sheet: -1.09 (0.36), residues: 189 loop : -1.16 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.008 0.001 TYR B 368 PHE 0.007 0.001 PHE B 124 TRP 0.006 0.001 TRP A 310 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 6101) covalent geometry : angle 0.54943 / 0.28 ( 8272) SS BOND : bond 0.00269 / 0.19 ( 16) SS BOND : angle 0.99491 / 0.56 ( 32) hydrogen bonds : bond 0.03627 / 2.36 ( 181) hydrogen bonds : angle 5.70150 / 4.12 ( 567) link_BETA1-4 : bond 0.00399 / 0.19 ( 8) link_BETA1-4 : angle 1.94532 / 1.03 ( 24) link_BETA1-6 : bond 0.00385 / 0.20 ( 2) link_BETA1-6 : angle 1.27732 / 0.53 ( 6) link_NAG-ASN : bond 0.00491 / 0.25 ( 5) link_NAG-ASN : angle 1.97420 / 0.94 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8363 (ptpt) cc_final: 0.7707 (pttp) REVERT: A 206 GLN cc_start: 0.7852 (tt0) cc_final: 0.7502 (mt0) REVERT: A 213 GLU cc_start: 0.7248 (tp30) cc_final: 0.6812 (tm-30) REVERT: A 382 MET cc_start: 0.8996 (mmm) cc_final: 0.8680 (mmm) REVERT: C 1361 ASN cc_start: 0.5949 (m-40) cc_final: 0.5206 (m-40) REVERT: C 1383 ASN cc_start: 0.7545 (p0) cc_final: 0.7059 (m-40) outliers start: 11 outliers final: 10 residues processed: 82 average time/residue: 0.2044 time to fit residues: 21.7710 Evaluate side-chains 84 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.162098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136121 restraints weight = 26396.622| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.36 r_work: 0.3450 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6132 Z= 0.133 Angle : 0.570 4.926 8349 Z= 0.282 Chirality : 0.040 0.151 947 Planarity : 0.004 0.062 1040 Dihedral : 5.709 58.026 1102 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 1.72 % Allowed : 21.28 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.31), residues: 707 helix: 0.56 (0.45), residues: 142 sheet: -1.10 (0.36), residues: 189 loop : -1.14 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 152 TYR 0.008 0.001 TYR B 368 PHE 0.009 0.001 PHE B 124 TRP 0.006 0.001 TRP A 310 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 6101) covalent geometry : angle 0.55156 / 0.28 ( 8272) SS BOND : bond 0.00321 / 0.22 ( 16) SS BOND : angle 1.03627 / 0.59 ( 32) hydrogen bonds : bond 0.03647 / 2.37 ( 181) hydrogen bonds : angle 5.70371 / 4.13 ( 567) link_BETA1-4 : bond 0.00376 / 0.18 ( 8) link_BETA1-4 : angle 1.91901 / 1.02 ( 24) link_BETA1-6 : bond 0.00369 / 0.19 ( 2) link_BETA1-6 : angle 1.27530 / 0.53 ( 6) link_NAG-ASN : bond 0.00489 / 0.25 ( 5) link_NAG-ASN : angle 1.99671 / 0.95 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7655 (pttp) REVERT: A 206 GLN cc_start: 0.7867 (tt0) cc_final: 0.7506 (mt0) REVERT: A 382 MET cc_start: 0.9004 (mmm) cc_final: 0.8696 (mmm) REVERT: C 1361 ASN cc_start: 0.6018 (m-40) cc_final: 0.5191 (m-40) REVERT: C 1383 ASN cc_start: 0.7534 (p0) cc_final: 0.7081 (m-40) outliers start: 11 outliers final: 11 residues processed: 82 average time/residue: 0.2061 time to fit residues: 21.9392 Evaluate side-chains 83 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 17 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137593 restraints weight = 22641.689| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.18 r_work: 0.3479 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6132 Z= 0.124 Angle : 0.563 4.818 8349 Z= 0.279 Chirality : 0.040 0.151 947 Planarity : 0.004 0.049 1040 Dihedral : 5.656 57.882 1102 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 1.88 % Allowed : 20.81 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.32), residues: 707 helix: 0.62 (0.45), residues: 142 sheet: -1.05 (0.36), residues: 189 loop : -1.11 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 180 TYR 0.009 0.001 TYR B 121 PHE 0.006 0.001 PHE B 217 TRP 0.006 0.001 TRP A 310 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 6101) covalent geometry : angle 0.54611 / 0.27 ( 8272) SS BOND : bond 0.00278 / 0.19 ( 16) SS BOND : angle 1.01208 / 0.57 ( 32) hydrogen bonds : bond 0.03578 / 2.34 ( 181) hydrogen bonds : angle 5.64783 / 4.09 ( 567) link_BETA1-4 : bond 0.00374 / 0.18 ( 8) link_BETA1-4 : angle 1.88123 / 1.00 ( 24) link_BETA1-6 : bond 0.00351 / 0.18 ( 2) link_BETA1-6 : angle 1.25198 / 0.51 ( 6) link_NAG-ASN : bond 0.00478 / 0.24 ( 5) link_NAG-ASN : angle 1.94439 / 0.93 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8229 (ptpt) cc_final: 0.7622 (pttp) REVERT: A 206 GLN cc_start: 0.7842 (tt0) cc_final: 0.7504 (mt0) REVERT: A 382 MET cc_start: 0.9011 (mmm) cc_final: 0.8705 (mmm) REVERT: C 1361 ASN cc_start: 0.5997 (m-40) cc_final: 0.5234 (m-40) REVERT: C 1383 ASN cc_start: 0.7467 (p0) cc_final: 0.7060 (m-40) outliers start: 12 outliers final: 11 residues processed: 84 average time/residue: 0.1910 time to fit residues: 20.9618 Evaluate side-chains 84 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.161482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134916 restraints weight = 27762.739| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.44 r_work: 0.3435 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6132 Z= 0.154 Angle : 0.580 5.061 8349 Z= 0.288 Chirality : 0.040 0.152 947 Planarity : 0.004 0.047 1040 Dihedral : 5.714 58.293 1102 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 2.03 % Allowed : 20.97 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.31), residues: 707 helix: 0.58 (0.45), residues: 142 sheet: -1.08 (0.36), residues: 189 loop : -1.16 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 180 TYR 0.012 0.001 TYR C1351 PHE 0.009 0.001 PHE B 124 TRP 0.007 0.001 TRP A 310 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 6101) covalent geometry : angle 0.56107 / 0.28 ( 8272) SS BOND : bond 0.00359 / 0.25 ( 16) SS BOND : angle 1.10342 / 0.63 ( 32) hydrogen bonds : bond 0.03693 / 2.39 ( 181) hydrogen bonds : angle 5.69906 / 4.13 ( 567) link_BETA1-4 : bond 0.00357 / 0.17 ( 8) link_BETA1-4 : angle 1.91002 / 1.02 ( 24) link_BETA1-6 : bond 0.00347 / 0.18 ( 2) link_BETA1-6 : angle 1.28258 / 0.53 ( 6) link_NAG-ASN : bond 0.00494 / 0.25 ( 5) link_NAG-ASN : angle 2.05868 / 0.97 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 334 is missing expected H atoms. Skipping. Residue LYS 1403 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8281 (ptpt) cc_final: 0.7656 (pttp) REVERT: A 206 GLN cc_start: 0.7888 (tt0) cc_final: 0.7519 (mt0) REVERT: A 382 MET cc_start: 0.9027 (mmm) cc_final: 0.8728 (mmm) REVERT: C 1361 ASN cc_start: 0.6182 (m-40) cc_final: 0.5425 (m-40) outliers start: 13 outliers final: 12 residues processed: 83 average time/residue: 0.1641 time to fit residues: 18.0026 Evaluate side-chains 86 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 359 GLN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain C residue 1374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135261 restraints weight = 30366.771| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.56 r_work: 0.3437 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6132 Z= 0.116 Angle : 0.559 4.778 8349 Z= 0.277 Chirality : 0.039 0.151 947 Planarity : 0.004 0.048 1040 Dihedral : 5.619 57.567 1102 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.03 % Allowed : 20.81 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.32), residues: 707 helix: 0.64 (0.45), residues: 142 sheet: -1.01 (0.36), residues: 189 loop : -1.08 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.013 0.001 TYR C1351 PHE 0.007 0.001 PHE B 124 TRP 0.006 0.001 TRP B 310 HIS 0.002 0.000 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6101) covalent geometry : angle 0.54182 / 0.27 ( 8272) SS BOND : bond 0.00265 / 0.18 ( 16) SS BOND : angle 0.96120 / 0.55 ( 32) hydrogen bonds : bond 0.03523 / 2.30 ( 181) hydrogen bonds : angle 5.60495 / 4.06 ( 567) link_BETA1-4 : bond 0.00381 / 0.19 ( 8) link_BETA1-4 : angle 1.84938 / 0.99 ( 24) link_BETA1-6 : bond 0.00362 / 0.19 ( 2) link_BETA1-6 : angle 1.25439 / 0.51 ( 6) link_NAG-ASN : bond 0.00491 / 0.25 ( 5) link_NAG-ASN : angle 1.91933 / 0.91 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.53 seconds wall clock time: 60 minutes 32.72 seconds (3632.72 seconds total)