Starting phenix.real_space_refine on Thu Jul 2 08:41:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lze_23605/07_2026/7lze_23605.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lze_23605/07_2026/7lze_23605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2026/7lze_23605.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2026/7lze_23605.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2026/7lze_23605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2026/7lze_23605.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2026/7lze_23605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2026/7lze_23605.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.091 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 69 5.16 5 C 4899 2.51 5 N 1314 2.21 5 O 1560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7842 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2572 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2572 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain breaks: 1 Chain: "C" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2572 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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 chiralities: 1 Time building chain proxies: 1.34, per 1000 atoms: 0.17 Number of scatterers: 7842 At special positions: 0 Unit cell: (88.7841, 86.5919, 107.418, 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 69 16.00 O 1560 8.00 N 1314 7.00 C 4899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 63 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS C 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 63 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.04 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.04 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 57 " " NAG B 601 " - " ASN B 57 " " NAG C 601 " - " ASN C 57 " " NAG D 1 " - " ASN A 353 " " NAG E 1 " - " ASN B 353 " " NAG F 1 " - " ASN C 353 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 313.9 milliseconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 16 sheets defined 25.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.716A pdb=" N GLU A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.545A pdb=" N MET A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.593A pdb=" N LEU A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.681A pdb=" N ARG A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 253' Processing helix chain 'A' and resid 348 through 353 removed outlier: 4.166A pdb=" N ILE A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 84 removed outlier: 3.990A pdb=" N THR B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.555A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.871A pdb=" N LEU B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.585A pdb=" N ARG B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 removed outlier: 4.028A pdb=" N ILE B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 84 removed outlier: 3.649A pdb=" N GLU C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.639A pdb=" N SER C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.643A pdb=" N LEU C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.718A pdb=" N ARG C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 253' Processing helix chain 'C' and resid 348 through 353 removed outlier: 4.118A pdb=" N ILE C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 4.231A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU A 36 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N THR A 281 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 38 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 279 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ARG A 40 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLY A 277 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY A 42 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 275 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 312 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 263 removed outlier: 7.080A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 47 " --> pdb=" O HIS C 435 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE C 437 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR A 49 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.514A pdb=" N SER A 291 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 303 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 376 removed outlier: 3.928A pdb=" N CYS A 384 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 406 " --> pdb=" O CYS A 384 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 393 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 438 removed outlier: 6.911A pdb=" N SER B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL B 262 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 21 through 24 removed outlier: 4.007A pdb=" N GLY B 34 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS B 283 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU B 36 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR B 281 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 38 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE B 279 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG B 40 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY B 277 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY B 42 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 275 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS B 312 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 21 through 24 removed outlier: 8.181A pdb=" N VAL B 333 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 36 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU B 327 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 291 through 294 removed outlier: 3.702A pdb=" N ALA B 300 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 303 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 372 through 376 removed outlier: 3.798A pdb=" N CYS B 384 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B 406 " --> pdb=" O CYS B 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 401 through 402 removed outlier: 3.912A pdb=" N LYS B 401 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 391 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 434 through 438 removed outlier: 6.959A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 257 " --> pdb=" O THR C 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 24 removed outlier: 4.236A pdb=" N GLY C 34 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N CYS C 283 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU C 36 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N THR C 281 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 38 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE C 279 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ARG C 40 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY C 277 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY C 42 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C 275 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS C 312 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 291 through 295 removed outlier: 3.506A pdb=" N SER C 291 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 303 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 372 through 376 removed outlier: 3.952A pdb=" N CYS C 384 " --> pdb=" O GLY C 406 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 406 " --> pdb=" O CYS C 384 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 390 through 393 293 hydrogen bonds defined for protein. 807 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: 0.87 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2565 1.35 - 1.47: 1823 1.47 - 1.59: 3487 1.59 - 1.72: 0 1.72 - 1.84: 90 Bond restraints: 7965 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 ... (remaining 7960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 10425 1.04 - 2.08: 285 2.08 - 3.12: 66 3.12 - 4.17: 21 4.17 - 5.21: 3 Bond angle restraints: 10800 Sorted by residual: angle pdb=" CA CYS C 283 " pdb=" CB CYS C 283 " pdb=" SG CYS C 283 " ideal model delta sigma weight residual 114.40 119.61 -5.21 2.30e+00 1.89e-01 5.13e+00 angle pdb=" CA CYS A 283 " pdb=" CB CYS A 283 " pdb=" SG CYS A 283 " ideal model delta sigma weight residual 114.40 119.55 -5.15 2.30e+00 1.89e-01 5.00e+00 angle pdb=" C SER A 355 " pdb=" N THR A 356 " pdb=" CA THR A 356 " ideal model delta sigma weight residual 121.54 125.17 -3.63 1.91e+00 2.74e-01 3.61e+00 angle pdb=" C SER C 355 " pdb=" N THR C 356 " pdb=" CA THR C 356 " ideal model delta sigma weight residual 121.54 125.12 -3.58 1.91e+00 2.74e-01 3.52e+00 angle pdb=" C SER B 355 " pdb=" N THR B 356 " pdb=" CA THR B 356 " ideal model delta sigma weight residual 121.54 125.06 -3.52 1.91e+00 2.74e-01 3.40e+00 ... (remaining 10795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 4331 17.13 - 34.27: 361 34.27 - 51.40: 109 51.40 - 68.53: 21 68.53 - 85.67: 11 Dihedral angle restraints: 4833 sinusoidal: 1902 harmonic: 2931 Sorted by residual: dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 63 " pdb=" CB CYS B 63 " ideal model delta sinusoidal sigma weight residual -86.00 -171.67 85.67 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS C 60 " pdb=" SG CYS C 60 " pdb=" SG CYS C 63 " pdb=" CB CYS C 63 " ideal model delta sinusoidal sigma weight residual 93.00 172.91 -79.91 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 63 " pdb=" CB CYS A 63 " ideal model delta sinusoidal sigma weight residual 93.00 172.51 -79.51 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 4830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 848 0.032 - 0.063: 279 0.063 - 0.095: 66 0.095 - 0.127: 94 0.127 - 0.158: 6 Chirality restraints: 1293 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CA VAL C 38 " pdb=" N VAL C 38 " pdb=" C VAL C 38 " pdb=" CB VAL C 38 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE A 285 " pdb=" N ILE A 285 " pdb=" C ILE A 285 " pdb=" CB ILE A 285 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1290 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 355 " 0.004 2.00e-02 2.50e+03 8.38e-03 7.02e-01 pdb=" C SER B 355 " -0.014 2.00e-02 2.50e+03 pdb=" O SER B 355 " 0.005 2.00e-02 2.50e+03 pdb=" N THR B 356 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 355 " 0.004 2.00e-02 2.50e+03 8.30e-03 6.89e-01 pdb=" C SER C 355 " -0.014 2.00e-02 2.50e+03 pdb=" O SER C 355 " 0.005 2.00e-02 2.50e+03 pdb=" N THR C 356 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 355 " 0.004 2.00e-02 2.50e+03 8.20e-03 6.73e-01 pdb=" C SER A 355 " -0.014 2.00e-02 2.50e+03 pdb=" O SER A 355 " 0.005 2.00e-02 2.50e+03 pdb=" N THR A 356 " 0.005 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1072 2.76 - 3.29: 7484 3.29 - 3.83: 11854 3.83 - 4.36: 14177 4.36 - 4.90: 26051 Nonbonded interactions: 60638 Sorted by model distance: nonbonded pdb=" OE1 GLN A 206 " pdb=" OG SER A 218 " model vdw 2.222 3.040 nonbonded pdb=" OE1 GLN C 206 " pdb=" OG SER C 218 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU B 305 " pdb=" OG SER B 364 " model vdw 2.272 3.040 nonbonded pdb=" OE2 GLU C 305 " pdb=" OG SER C 364 " model vdw 2.286 3.040 nonbonded pdb=" OE1 GLN B 206 " pdb=" OG SER B 218 " model vdw 2.302 3.040 ... (remaining 60633 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.930 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.003 0.029 7998 Z= 0.130 Angle : 0.458 5.208 10875 Z= 0.243 Chirality : 0.043 0.158 1293 Planarity : 0.002 0.020 1368 Dihedral : 13.894 82.348 2877 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.28), residues: 999 helix: 2.96 (0.38), residues: 225 sheet: -1.15 (0.32), residues: 285 loop : -1.74 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.008 0.001 TYR A 310 PHE 0.003 0.000 PHE A 334 TRP 0.002 0.000 TRP A 43 HIS 0.001 0.000 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 7965) covalent geometry : angle 0.45284 / 0.24 (10800) SS BOND : bond 0.00330 / 0.23 ( 24) SS BOND : angle 0.93719 / 0.61 ( 48) hydrogen bonds : bond 0.25335 / 16.57 ( 289) hydrogen bonds : angle 8.45432 / 6.14 ( 807) link_BETA1-4 : bond 0.00294 / 0.15 ( 3) link_BETA1-4 : angle 0.80386 / 0.38 ( 9) link_NAG-ASN : bond 0.00157 / 0.09 ( 6) link_NAG-ASN : angle 1.09301 / 0.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: C 189 MET cc_start: 0.7566 (mtt) cc_final: 0.6877 (mtt) REVERT: C 270 MET cc_start: 0.7362 (ttm) cc_final: 0.7162 (ttm) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.0460 time to fit residues: 3.8561 Evaluate side-chains 39 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.0050 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.118169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098442 restraints weight = 11688.371| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.66 r_work: 0.3177 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7998 Z= 0.155 Angle : 0.584 9.657 10875 Z= 0.304 Chirality : 0.047 0.243 1293 Planarity : 0.003 0.020 1368 Dihedral : 4.136 19.608 1092 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.46 % Allowed : 5.27 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.27), residues: 999 helix: 2.39 (0.35), residues: 231 sheet: -0.92 (0.32), residues: 294 loop : -1.75 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 248 TYR 0.018 0.001 TYR B 319 PHE 0.006 0.001 PHE B 200 TRP 0.006 0.001 TRP A 309 HIS 0.002 0.001 HIS C 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 ( 7965) covalent geometry : angle 0.57683 / 0.30 (10800) SS BOND : bond 0.00595 / 0.42 ( 24) SS BOND : angle 1.29168 / 0.79 ( 48) hydrogen bonds : bond 0.04593 / 2.90 ( 289) hydrogen bonds : angle 5.67736 / 4.11 ( 807) link_BETA1-4 : bond 0.00394 / 0.20 ( 3) link_BETA1-4 : angle 0.84756 / 0.41 ( 9) link_NAG-ASN : bond 0.00845 / 0.43 ( 6) link_NAG-ASN : angle 1.27513 / 0.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ASN cc_start: 0.7282 (OUTLIER) cc_final: 0.6999 (m-40) outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.0555 time to fit residues: 4.6935 Evaluate side-chains 42 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 55 optimal weight: 0.0020 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.119135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099380 restraints weight = 11677.388| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.67 r_work: 0.3185 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7998 Z= 0.112 Angle : 0.535 9.541 10875 Z= 0.278 Chirality : 0.045 0.240 1293 Planarity : 0.003 0.022 1368 Dihedral : 4.081 18.734 1092 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.92 % Allowed : 9.05 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.27), residues: 999 helix: 2.35 (0.35), residues: 231 sheet: -0.80 (0.32), residues: 294 loop : -1.68 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 367 TYR 0.018 0.001 TYR C 319 PHE 0.005 0.001 PHE B 200 TRP 0.003 0.001 TRP A 309 HIS 0.002 0.000 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 7965) covalent geometry : angle 0.52758 / 0.28 (10800) SS BOND : bond 0.00566 / 0.41 ( 24) SS BOND : angle 1.23739 / 0.77 ( 48) hydrogen bonds : bond 0.03679 / 2.33 ( 289) hydrogen bonds : angle 5.15128 / 3.75 ( 807) link_BETA1-4 : bond 0.00460 / 0.23 ( 3) link_BETA1-4 : angle 0.89824 / 0.43 ( 9) link_NAG-ASN : bond 0.00552 / 0.29 ( 6) link_NAG-ASN : angle 1.17866 / 0.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8944 (mtm) cc_final: 0.8633 (mtm) REVERT: B 57 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6854 (m-40) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 0.0639 time to fit residues: 5.1445 Evaluate side-chains 45 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain C residue 410 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.118085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098488 restraints weight = 11727.013| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.65 r_work: 0.3170 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7998 Z= 0.129 Angle : 0.552 9.666 10875 Z= 0.286 Chirality : 0.045 0.244 1293 Planarity : 0.003 0.023 1368 Dihedral : 4.118 18.665 1092 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.37 % Allowed : 9.28 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.27), residues: 999 helix: 2.34 (0.35), residues: 231 sheet: -0.63 (0.33), residues: 279 loop : -1.79 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 253 TYR 0.021 0.001 TYR B 319 PHE 0.005 0.001 PHE B 256 TRP 0.003 0.001 TRP A 284 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 7965) covalent geometry : angle 0.54411 / 0.28 (10800) SS BOND : bond 0.00594 / 0.43 ( 24) SS BOND : angle 1.33719 / 0.82 ( 48) hydrogen bonds : bond 0.03509 / 2.21 ( 289) hydrogen bonds : angle 4.88547 / 3.56 ( 807) link_BETA1-4 : bond 0.00418 / 0.21 ( 3) link_BETA1-4 : angle 0.92145 / 0.45 ( 9) link_NAG-ASN : bond 0.00507 / 0.27 ( 6) link_NAG-ASN : angle 1.25106 / 0.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8957 (mtm) cc_final: 0.8639 (mtm) REVERT: C 319 TYR cc_start: 0.8601 (t80) cc_final: 0.8391 (t80) outliers start: 12 outliers final: 11 residues processed: 51 average time/residue: 0.0434 time to fit residues: 3.6309 Evaluate side-chains 51 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 417 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098133 restraints weight = 11758.950| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.66 r_work: 0.3160 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7998 Z= 0.134 Angle : 0.550 9.655 10875 Z= 0.285 Chirality : 0.045 0.242 1293 Planarity : 0.003 0.023 1368 Dihedral : 4.161 18.662 1092 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.95 % Allowed : 10.65 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.27), residues: 999 helix: 2.36 (0.35), residues: 231 sheet: -0.63 (0.33), residues: 279 loop : -1.86 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 253 TYR 0.022 0.001 TYR B 319 PHE 0.005 0.001 PHE B 256 TRP 0.003 0.001 TRP A 284 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 7965) covalent geometry : angle 0.54023 / 0.28 (10800) SS BOND : bond 0.00616 / 0.44 ( 24) SS BOND : angle 1.35657 / 0.85 ( 48) hydrogen bonds : bond 0.03397 / 2.14 ( 289) hydrogen bonds : angle 4.75054 / 3.46 ( 807) link_BETA1-4 : bond 0.00488 / 0.24 ( 3) link_BETA1-4 : angle 0.98862 / 0.47 ( 9) link_NAG-ASN : bond 0.00398 / 0.22 ( 6) link_NAG-ASN : angle 1.45990 / 0.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8974 (mtm) cc_final: 0.8666 (mtm) outliers start: 17 outliers final: 13 residues processed: 57 average time/residue: 0.0523 time to fit residues: 4.9679 Evaluate side-chains 53 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.118187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098568 restraints weight = 11694.826| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.66 r_work: 0.3180 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7998 Z= 0.116 Angle : 0.528 9.650 10875 Z= 0.274 Chirality : 0.044 0.242 1293 Planarity : 0.003 0.024 1368 Dihedral : 4.098 18.552 1092 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.95 % Allowed : 11.80 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.27), residues: 999 helix: 2.39 (0.35), residues: 231 sheet: -0.52 (0.35), residues: 252 loop : -1.83 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 253 TYR 0.019 0.001 TYR A 319 PHE 0.004 0.001 PHE B 256 TRP 0.003 0.001 TRP A 43 HIS 0.002 0.000 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7965) covalent geometry : angle 0.51919 / 0.27 (10800) SS BOND : bond 0.00592 / 0.43 ( 24) SS BOND : angle 1.33016 / 0.83 ( 48) hydrogen bonds : bond 0.03135 / 1.98 ( 289) hydrogen bonds : angle 4.62348 / 3.37 ( 807) link_BETA1-4 : bond 0.00428 / 0.21 ( 3) link_BETA1-4 : angle 0.98035 / 0.46 ( 9) link_NAG-ASN : bond 0.00250 / 0.16 ( 6) link_NAG-ASN : angle 1.12531 / 0.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8934 (mtm) cc_final: 0.8613 (mtm) outliers start: 17 outliers final: 17 residues processed: 61 average time/residue: 0.0545 time to fit residues: 5.5713 Evaluate side-chains 58 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.116920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097307 restraints weight = 11771.205| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.67 r_work: 0.3151 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7998 Z= 0.145 Angle : 0.553 9.689 10875 Z= 0.286 Chirality : 0.045 0.244 1293 Planarity : 0.003 0.025 1368 Dihedral : 4.196 18.593 1092 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.06 % Allowed : 12.49 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.27), residues: 999 helix: 2.40 (0.35), residues: 231 sheet: -0.71 (0.32), residues: 285 loop : -1.95 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 253 TYR 0.022 0.001 TYR B 319 PHE 0.005 0.001 PHE B 256 TRP 0.003 0.001 TRP A 284 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.14 ( 7965) covalent geometry : angle 0.54365 / 0.28 (10800) SS BOND : bond 0.00626 / 0.45 ( 24) SS BOND : angle 1.43902 / 0.90 ( 48) hydrogen bonds : bond 0.03337 / 2.13 ( 289) hydrogen bonds : angle 4.60715 / 3.36 ( 807) link_BETA1-4 : bond 0.00463 / 0.23 ( 3) link_BETA1-4 : angle 1.01780 / 0.48 ( 9) link_NAG-ASN : bond 0.00299 / 0.18 ( 6) link_NAG-ASN : angle 1.08942 / 0.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8992 (mtm) cc_final: 0.8667 (mtm) outliers start: 18 outliers final: 18 residues processed: 60 average time/residue: 0.0481 time to fit residues: 4.8255 Evaluate side-chains 64 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.117585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098064 restraints weight = 11783.240| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.66 r_work: 0.3168 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7998 Z= 0.117 Angle : 0.531 9.653 10875 Z= 0.275 Chirality : 0.044 0.242 1293 Planarity : 0.003 0.023 1368 Dihedral : 4.125 18.453 1092 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.52 % Allowed : 12.14 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.27), residues: 999 helix: 2.45 (0.35), residues: 231 sheet: -0.54 (0.32), residues: 279 loop : -1.95 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 253 TYR 0.025 0.001 TYR A 319 PHE 0.005 0.001 PHE B 256 TRP 0.003 0.001 TRP A 43 HIS 0.002 0.000 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7965) covalent geometry : angle 0.52263 / 0.27 (10800) SS BOND : bond 0.00591 / 0.43 ( 24) SS BOND : angle 1.36215 / 0.85 ( 48) hydrogen bonds : bond 0.03068 / 1.94 ( 289) hydrogen bonds : angle 4.53489 / 3.32 ( 807) link_BETA1-4 : bond 0.00411 / 0.20 ( 3) link_BETA1-4 : angle 0.99923 / 0.47 ( 9) link_NAG-ASN : bond 0.00282 / 0.18 ( 6) link_NAG-ASN : angle 1.07850 / 0.54 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8941 (mtm) cc_final: 0.8625 (mtm) outliers start: 22 outliers final: 21 residues processed: 63 average time/residue: 0.0504 time to fit residues: 5.3144 Evaluate side-chains 64 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 0.0270 chunk 98 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9440 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.118531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098286 restraints weight = 11845.464| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.73 r_work: 0.3148 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7998 Z= 0.137 Angle : 0.542 9.688 10875 Z= 0.281 Chirality : 0.045 0.244 1293 Planarity : 0.003 0.025 1368 Dihedral : 4.175 18.433 1092 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.98 % Allowed : 11.80 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.27), residues: 999 helix: 2.43 (0.35), residues: 231 sheet: -0.85 (0.32), residues: 288 loop : -1.86 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 253 TYR 0.020 0.001 TYR B 319 PHE 0.005 0.001 PHE B 256 TRP 0.003 0.001 TRP A 43 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 7965) covalent geometry : angle 0.53369 / 0.28 (10800) SS BOND : bond 0.00605 / 0.43 ( 24) SS BOND : angle 1.37997 / 0.86 ( 48) hydrogen bonds : bond 0.03173 / 2.02 ( 289) hydrogen bonds : angle 4.52917 / 3.31 ( 807) link_BETA1-4 : bond 0.00439 / 0.22 ( 3) link_BETA1-4 : angle 1.02103 / 0.48 ( 9) link_NAG-ASN : bond 0.00270 / 0.17 ( 6) link_NAG-ASN : angle 1.11087 / 0.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8936 (mtm) cc_final: 0.8626 (mtm) outliers start: 26 outliers final: 21 residues processed: 65 average time/residue: 0.0501 time to fit residues: 5.5046 Evaluate side-chains 64 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.116003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097210 restraints weight = 11527.645| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.49 r_work: 0.3183 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7998 Z= 0.122 Angle : 0.544 10.398 10875 Z= 0.281 Chirality : 0.044 0.243 1293 Planarity : 0.003 0.024 1368 Dihedral : 4.134 18.413 1092 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.63 % Allowed : 12.49 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.27), residues: 999 helix: 2.44 (0.35), residues: 231 sheet: -0.48 (0.33), residues: 273 loop : -1.96 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 253 TYR 0.017 0.001 TYR B 319 PHE 0.004 0.001 PHE B 256 TRP 0.003 0.001 TRP A 43 HIS 0.002 0.000 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 7965) covalent geometry : angle 0.52636 / 0.27 (10800) SS BOND : bond 0.00670 / 0.48 ( 24) SS BOND : angle 2.00363 / 1.20 ( 48) hydrogen bonds : bond 0.03013 / 1.93 ( 289) hydrogen bonds : angle 4.49135 / 3.29 ( 807) link_BETA1-4 : bond 0.00451 / 0.23 ( 3) link_BETA1-4 : angle 1.02112 / 0.48 ( 9) link_NAG-ASN : bond 0.00278 / 0.17 ( 6) link_NAG-ASN : angle 1.10113 / 0.55 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 44 time to evaluate : 0.181 Fit side-chains REVERT: A 244 MET cc_start: 0.8965 (mtm) cc_final: 0.8651 (mtm) outliers start: 23 outliers final: 21 residues processed: 62 average time/residue: 0.0571 time to fit residues: 5.6466 Evaluate side-chains 63 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 385 TYR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.115188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095634 restraints weight = 11853.213| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.66 r_work: 0.3119 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7998 Z= 0.195 Angle : 0.606 10.451 10875 Z= 0.312 Chirality : 0.046 0.245 1293 Planarity : 0.003 0.027 1368 Dihedral : 4.404 19.164 1092 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.41 % Allowed : 12.83 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.27), residues: 999 helix: 2.33 (0.34), residues: 231 sheet: -0.82 (0.31), residues: 303 loop : -1.98 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 253 TYR 0.022 0.001 TYR B 319 PHE 0.006 0.001 PHE C 207 TRP 0.004 0.001 TRP A 284 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.19 ( 7965) covalent geometry : angle 0.59007 / 0.31 (10800) SS BOND : bond 0.00748 / 0.53 ( 24) SS BOND : angle 2.04728 / 1.24 ( 48) hydrogen bonds : bond 0.03589 / 2.30 ( 289) hydrogen bonds : angle 4.61569 / 3.37 ( 807) link_BETA1-4 : bond 0.00451 / 0.23 ( 3) link_BETA1-4 : angle 1.10247 / 0.51 ( 9) link_NAG-ASN : bond 0.00234 / 0.14 ( 6) link_NAG-ASN : angle 1.20522 / 0.60 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1465.43 seconds wall clock time: 25 minutes 57.74 seconds (1557.74 seconds total)