Starting phenix.real_space_refine on Fri Jul 25 18:28:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lze_23605/07_2025/7lze_23605.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lze_23605/07_2025/7lze_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2025/7lze_23605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2025/7lze_23605.map" model { file = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2025/7lze_23605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lze_23605/07_2025/7lze_23605.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.25, per 1000 atoms: 0.67 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: 2.06 Conformation dependent library (CDL) restraints added in 909.7 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: 0.90 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: 2.05 Time building geometry restraints manager: 2.42 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: 4494 17.13 - 34.27: 369 34.27 - 51.40: 127 51.40 - 68.53: 21 68.53 - 85.67: 11 Dihedral angle restraints: 5022 sinusoidal: 2091 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 5019 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: 0.03 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.260 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 13.958 82.348 3066 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.40 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.000 TRP A 43 HIS 0.001 0.000 HIS B 435 PHE 0.003 0.000 PHE A 334 TYR 0.008 0.001 TYR A 310 ARG 0.002 0.000 ARG B 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 6) link_NAG-ASN : angle 1.09301 ( 18) link_BETA1-4 : bond 0.00294 ( 3) link_BETA1-4 : angle 0.80386 ( 9) hydrogen bonds : bond 0.25335 ( 289) hydrogen bonds : angle 8.45432 ( 807) SS BOND : bond 0.00330 ( 24) SS BOND : angle 0.93719 ( 48) covalent geometry : bond 0.00272 ( 7965) covalent geometry : angle 0.45284 (10800) *********************** 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 : 0.959 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: 0.1483 time to fit residues: 12.1875 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 : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097515 restraints weight = 11648.497| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.65 r_work: 0.3158 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7998 Z= 0.181 Angle : 0.597 9.365 10875 Z= 0.311 Chirality : 0.047 0.202 1293 Planarity : 0.003 0.021 1368 Dihedral : 6.709 55.082 1281 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.46 % Allowed : 5.73 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.27), residues: 999 helix: 2.38 (0.35), residues: 231 sheet: -0.96 (0.32), residues: 294 loop : -1.77 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.002 0.001 HIS B 435 PHE 0.006 0.001 PHE B 200 TYR 0.019 0.001 TYR B 319 ARG 0.002 0.000 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00848 ( 6) link_NAG-ASN : angle 1.35600 ( 18) link_BETA1-4 : bond 0.00415 ( 3) link_BETA1-4 : angle 1.13159 ( 9) hydrogen bonds : bond 0.04832 ( 289) hydrogen bonds : angle 5.72440 ( 807) SS BOND : bond 0.00635 ( 24) SS BOND : angle 1.37720 ( 48) covalent geometry : bond 0.00447 ( 7965) covalent geometry : angle 0.58857 (10800) *********************** 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 53 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.6995 (m-40) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.1595 time to fit residues: 12.6433 Evaluate side-chains 41 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 73 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.0170 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 92 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100120 restraints weight = 11703.881| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.66 r_work: 0.3198 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7998 Z= 0.101 Angle : 0.525 9.531 10875 Z= 0.274 Chirality : 0.045 0.231 1293 Planarity : 0.003 0.021 1368 Dihedral : 6.330 54.786 1281 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.80 % Allowed : 8.59 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 999 helix: 2.38 (0.35), residues: 231 sheet: -0.82 (0.32), residues: 294 loop : -1.66 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 309 HIS 0.002 0.000 HIS B 435 PHE 0.005 0.001 PHE B 256 TYR 0.017 0.001 TYR B 319 ARG 0.001 0.000 ARG C 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 6) link_NAG-ASN : angle 1.18233 ( 18) link_BETA1-4 : bond 0.00443 ( 3) link_BETA1-4 : angle 1.24595 ( 9) hydrogen bonds : bond 0.03544 ( 289) hydrogen bonds : angle 5.11827 ( 807) SS BOND : bond 0.00550 ( 24) SS BOND : angle 1.21792 ( 48) covalent geometry : bond 0.00225 ( 7965) covalent geometry : angle 0.51751 (10800) *********************** 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 55 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8883 (mtm) cc_final: 0.8602 (mtm) REVERT: B 57 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.6895 (m-40) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 0.1612 time to fit residues: 13.5884 Evaluate side-chains 44 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 410 ILE 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 84 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 18 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098460 restraints weight = 11651.684| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.64 r_work: 0.3170 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7998 Z= 0.132 Angle : 0.559 9.742 10875 Z= 0.289 Chirality : 0.045 0.240 1293 Planarity : 0.003 0.022 1368 Dihedral : 6.224 54.971 1281 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.49 % Allowed : 9.39 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.27), residues: 999 helix: 2.37 (0.35), residues: 231 sheet: -0.62 (0.33), residues: 279 loop : -1.76 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 43 HIS 0.002 0.001 HIS B 435 PHE 0.004 0.001 PHE B 256 TYR 0.021 0.001 TYR B 319 ARG 0.001 0.000 ARG A 367 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 6) link_NAG-ASN : angle 1.33767 ( 18) link_BETA1-4 : bond 0.00484 ( 3) link_BETA1-4 : angle 1.26056 ( 9) hydrogen bonds : bond 0.03516 ( 289) hydrogen bonds : angle 4.87102 ( 807) SS BOND : bond 0.00587 ( 24) SS BOND : angle 1.31706 ( 48) covalent geometry : bond 0.00318 ( 7965) covalent geometry : angle 0.54964 (10800) *********************** 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 56 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8958 (mtm) cc_final: 0.8654 (mtm) REVERT: C 319 TYR cc_start: 0.8585 (t80) cc_final: 0.8325 (t80) outliers start: 13 outliers final: 12 residues processed: 50 average time/residue: 0.1378 time to fit residues: 11.5275 Evaluate side-chains 52 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 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 270 MET 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 53 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3551 r_free = 0.3551 target = 0.115916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096377 restraints weight = 11690.392| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.64 r_work: 0.3137 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7998 Z= 0.172 Angle : 0.581 9.754 10875 Z= 0.300 Chirality : 0.046 0.238 1293 Planarity : 0.003 0.024 1368 Dihedral : 6.245 54.737 1281 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.29 % Allowed : 10.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.27), residues: 999 helix: 2.29 (0.35), residues: 231 sheet: -1.00 (0.32), residues: 294 loop : -1.75 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 284 HIS 0.002 0.001 HIS B 435 PHE 0.005 0.001 PHE A 256 TYR 0.020 0.001 TYR B 319 ARG 0.002 0.000 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 6) link_NAG-ASN : angle 1.53851 ( 18) link_BETA1-4 : bond 0.00471 ( 3) link_BETA1-4 : angle 1.31753 ( 9) hydrogen bonds : bond 0.03660 ( 289) hydrogen bonds : angle 4.82474 ( 807) SS BOND : bond 0.00665 ( 24) SS BOND : angle 1.46053 ( 48) covalent geometry : bond 0.00428 ( 7965) covalent geometry : angle 0.57062 (10800) *********************** 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 65 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.967 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 58 average time/residue: 0.1345 time to fit residues: 12.9735 Evaluate side-chains 55 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 417 THR Chi-restraints excluded: chain C residue 26 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.117099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097595 restraints weight = 11664.168| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.65 r_work: 0.3156 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7998 Z= 0.125 Angle : 0.557 10.576 10875 Z= 0.287 Chirality : 0.044 0.236 1293 Planarity : 0.003 0.024 1368 Dihedral : 6.159 54.865 1281 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.18 % Allowed : 11.80 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 999 helix: 2.35 (0.35), residues: 231 sheet: -0.85 (0.34), residues: 261 loop : -1.73 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 43 HIS 0.002 0.000 HIS B 435 PHE 0.005 0.001 PHE B 256 TYR 0.021 0.001 TYR B 319 ARG 0.001 0.000 ARG C 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 6) link_NAG-ASN : angle 1.14239 ( 18) link_BETA1-4 : bond 0.00462 ( 3) link_BETA1-4 : angle 1.29937 ( 9) hydrogen bonds : bond 0.03195 ( 289) hydrogen bonds : angle 4.67693 ( 807) SS BOND : bond 0.00780 ( 24) SS BOND : angle 2.44640 ( 48) covalent geometry : bond 0.00307 ( 7965) covalent geometry : angle 0.53150 (10800) *********************** 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 62 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8973 (mtm) cc_final: 0.8660 (mtm) outliers start: 19 outliers final: 17 residues processed: 56 average time/residue: 0.1342 time to fit residues: 12.4385 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 : 0.921 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095927 restraints weight = 11853.924| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.66 r_work: 0.3130 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7998 Z= 0.177 Angle : 0.589 9.991 10875 Z= 0.302 Chirality : 0.046 0.238 1293 Planarity : 0.003 0.026 1368 Dihedral : 6.198 54.741 1281 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 999 helix: 2.26 (0.34), residues: 231 sheet: -0.94 (0.32), residues: 288 loop : -1.88 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 43 HIS 0.002 0.001 HIS B 435 PHE 0.005 0.001 PHE C 207 TYR 0.025 0.001 TYR B 319 ARG 0.002 0.000 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 6) link_NAG-ASN : angle 1.18118 ( 18) link_BETA1-4 : bond 0.00480 ( 3) link_BETA1-4 : angle 1.31348 ( 9) hydrogen bonds : bond 0.03521 ( 289) hydrogen bonds : angle 4.69904 ( 807) SS BOND : bond 0.00748 ( 24) SS BOND : angle 2.30727 ( 48) covalent geometry : bond 0.00445 ( 7965) covalent geometry : angle 0.56734 (10800) *********************** 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: 22 poor density : 43 time to evaluate : 0.951 Fit side-chains REVERT: A 244 MET cc_start: 0.9011 (mtm) cc_final: 0.8694 (mtm) REVERT: C 310 TYR cc_start: 0.8474 (m-80) cc_final: 0.8247 (m-80) outliers start: 22 outliers final: 19 residues processed: 59 average time/residue: 0.1353 time to fit residues: 13.2939 Evaluate side-chains 60 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 0.0070 chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097323 restraints weight = 11834.341| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.67 r_work: 0.3151 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7998 Z= 0.121 Angle : 0.558 11.122 10875 Z= 0.286 Chirality : 0.044 0.235 1293 Planarity : 0.003 0.025 1368 Dihedral : 6.114 54.928 1281 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.86 % Allowed : 11.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.27), residues: 999 helix: 2.38 (0.35), residues: 231 sheet: -0.76 (0.32), residues: 288 loop : -1.89 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 43 HIS 0.001 0.000 HIS B 435 PHE 0.004 0.001 PHE B 256 TYR 0.014 0.001 TYR B 319 ARG 0.001 0.000 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 6) link_NAG-ASN : angle 1.12102 ( 18) link_BETA1-4 : bond 0.00456 ( 3) link_BETA1-4 : angle 1.26224 ( 9) hydrogen bonds : bond 0.03033 ( 289) hydrogen bonds : angle 4.58554 ( 807) SS BOND : bond 0.00842 ( 24) SS BOND : angle 2.80060 ( 48) covalent geometry : bond 0.00294 ( 7965) covalent geometry : angle 0.52460 (10800) *********************** 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 73 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.912 Fit side-chains REVERT: A 26 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: A 244 MET cc_start: 0.8971 (mtm) cc_final: 0.8653 (mtm) REVERT: C 310 TYR cc_start: 0.8438 (m-80) cc_final: 0.8204 (m-80) outliers start: 25 outliers final: 21 residues processed: 68 average time/residue: 0.1253 time to fit residues: 14.0687 Evaluate side-chains 64 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU 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 29 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096693 restraints weight = 11866.729| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.65 r_work: 0.3147 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7998 Z= 0.139 Angle : 0.577 12.018 10875 Z= 0.294 Chirality : 0.044 0.237 1293 Planarity : 0.003 0.025 1368 Dihedral : 6.112 54.926 1281 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.75 % Allowed : 12.26 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.27), residues: 999 helix: 2.35 (0.35), residues: 231 sheet: -0.95 (0.32), residues: 294 loop : -1.84 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 43 HIS 0.002 0.001 HIS B 435 PHE 0.005 0.001 PHE B 256 TYR 0.027 0.001 TYR A 319 ARG 0.001 0.000 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 1.14726 ( 18) link_BETA1-4 : bond 0.00455 ( 3) link_BETA1-4 : angle 1.24239 ( 9) hydrogen bonds : bond 0.03103 ( 289) hydrogen bonds : angle 4.55934 ( 807) SS BOND : bond 0.00892 ( 24) SS BOND : angle 3.10376 ( 48) covalent geometry : bond 0.00345 ( 7965) covalent geometry : angle 0.53739 (10800) *********************** 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 67 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.866 Fit side-chains REVERT: A 26 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: A 244 MET cc_start: 0.8989 (mtm) cc_final: 0.8685 (mtm) REVERT: C 310 TYR cc_start: 0.8454 (m-80) cc_final: 0.8219 (m-80) outliers start: 24 outliers final: 23 residues processed: 60 average time/residue: 0.1333 time to fit residues: 13.1675 Evaluate side-chains 66 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 THR 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 417 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096828 restraints weight = 11899.383| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.65 r_work: 0.3149 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7998 Z= 0.134 Angle : 0.575 11.821 10875 Z= 0.293 Chirality : 0.044 0.236 1293 Planarity : 0.003 0.024 1368 Dihedral : 6.108 54.989 1281 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.75 % Allowed : 12.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.27), residues: 999 helix: 2.36 (0.35), residues: 231 sheet: -0.63 (0.32), residues: 279 loop : -1.97 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 43 HIS 0.002 0.000 HIS B 435 PHE 0.005 0.001 PHE B 256 TYR 0.019 0.001 TYR B 319 ARG 0.001 0.000 ARG C 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 1.14056 ( 18) link_BETA1-4 : bond 0.00455 ( 3) link_BETA1-4 : angle 1.22920 ( 9) hydrogen bonds : bond 0.03050 ( 289) hydrogen bonds : angle 4.51506 ( 807) SS BOND : bond 0.00899 ( 24) SS BOND : angle 3.03456 ( 48) covalent geometry : bond 0.00331 ( 7965) covalent geometry : angle 0.53771 (10800) ********************** 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 69 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.876 Fit side-chains REVERT: A 26 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: A 244 MET cc_start: 0.8983 (mtm) cc_final: 0.8671 (mtm) REVERT: C 310 TYR cc_start: 0.8445 (m-80) cc_final: 0.8207 (m-80) outliers start: 24 outliers final: 23 residues processed: 62 average time/residue: 0.1277 time to fit residues: 13.0317 Evaluate side-chains 67 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 THR 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 417 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.098556 restraints weight = 11788.781| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.65 r_work: 0.3175 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7998 Z= 0.107 Angle : 0.559 11.558 10875 Z= 0.286 Chirality : 0.044 0.234 1293 Planarity : 0.003 0.024 1368 Dihedral : 6.048 55.076 1281 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.98 % Allowed : 12.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.27), residues: 999 helix: 2.44 (0.35), residues: 231 sheet: -0.51 (0.33), residues: 273 loop : -1.93 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 43 HIS 0.001 0.000 HIS B 435 PHE 0.004 0.001 PHE B 256 TYR 0.016 0.001 TYR B 319 ARG 0.001 0.000 ARG B 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 6) link_NAG-ASN : angle 1.09309 ( 18) link_BETA1-4 : bond 0.00482 ( 3) link_BETA1-4 : angle 1.18095 ( 9) hydrogen bonds : bond 0.02797 ( 289) hydrogen bonds : angle 4.44974 ( 807) SS BOND : bond 0.00847 ( 24) SS BOND : angle 2.96323 ( 48) covalent geometry : bond 0.00255 ( 7965) covalent geometry : angle 0.52242 (10800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3673.94 seconds wall clock time: 63 minutes 51.82 seconds (3831.82 seconds total)