Starting phenix.real_space_refine on Mon Aug 25 02:40:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ore_70773/08_2025/9ore_70773_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ore_70773/08_2025/9ore_70773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ore_70773/08_2025/9ore_70773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ore_70773/08_2025/9ore_70773.map" model { file = "/net/cci-nas-00/data/ceres_data/9ore_70773/08_2025/9ore_70773_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ore_70773/08_2025/9ore_70773_neut_trim.cif" } resolution = 4.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 74 5.16 5 C 7491 2.51 5 N 2025 2.21 5 O 2344 1.98 5 H 11842 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23776 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 6679 Classifications: {'peptide': 437} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Chain: "B" Number of atoms: 6696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6696 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 423} Chain breaks: 1 Chain: "C" Number of atoms: 6721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6721 Classifications: {'peptide': 439} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 424} Chain breaks: 1 Chain: "H" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1847 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1724 Classifications: {'peptide': 113} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 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: 4.92, per 1000 atoms: 0.21 Number of scatterers: 23776 At special positions: 0 Unit cell: (88.638, 88.638, 150.348, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 O 2344 8.00 N 2025 7.00 C 7491 6.00 H 11842 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.06 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=1.99 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.19 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.30 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.06 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.23 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.19 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 182 " distance=2.25 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.24 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=1.87 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.06 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.30 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.07 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 182 " distance=2.20 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.26 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.22 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.01 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.28 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 501 " - " ASN A 57 " " NAG B 501 " - " ASN B 57 " " NAG C 501 " - " ASN C 172 " " NAG D 1 " - " ASN A 172 " " NAG E 1 " - " ASN B 172 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 599.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 25 sheets defined 30.2% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.674A pdb=" N GLU A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 111 through 130 removed outlier: 3.516A pdb=" N ALA A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.607A pdb=" N VAL A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 197 through 210 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.573A pdb=" N ASN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.534A pdb=" N GLU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 removed outlier: 3.701A pdb=" N LYS A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 460 through 467 removed outlier: 3.788A pdb=" N PHE A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.713A pdb=" N LEU B 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.585A pdb=" N ALA B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.682A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 344 through 352 removed outlier: 4.351A pdb=" N GLU B 349 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N CYS B 350 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 460 through 467 Processing helix chain 'C' and resid 53 through 58 removed outlier: 4.494A pdb=" N GLU C 56 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 82 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 111 through 130 removed outlier: 3.504A pdb=" N ALA C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 187 through 211 removed outlier: 3.997A pdb=" N VAL C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.520A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.614A pdb=" N LYS C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 324 No H-bonds generated for 'chain 'C' and resid 322 through 324' Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 345 through 350 removed outlier: 4.292A pdb=" N GLU C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS C 350 " --> pdb=" O GLN C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 345 through 350' Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 460 through 467 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.985A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 329 removed outlier: 8.210A pdb=" N VAL A 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 36 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A 36 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N THR A 281 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 38 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 279 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN A 312 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 286 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 308 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 317 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 329 removed outlier: 8.210A pdb=" N VAL A 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 36 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A 29 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.516A pdb=" N THR A 45 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 269 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL A 262 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 268 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.677A pdb=" N LEU A 302 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.596A pdb=" N MET A 372 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 398 through 402 removed outlier: 7.018A pdb=" N ILE A 392 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN A 402 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N CYS A 390 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.860A pdb=" N THR B 317 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP B 309 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 29 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 39 removed outlier: 6.240A pdb=" N LEU B 36 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N CYS B 335 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N VAL B 38 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.391A pdb=" N THR B 45 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR B 160 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL B 47 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL B 162 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 49 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 262 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 304 removed outlier: 3.601A pdb=" N SER B 364 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 372 through 376 removed outlier: 4.168A pdb=" N MET B 372 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 383 " --> pdb=" O MET B 372 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS B 384 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 398 through 402 removed outlier: 7.013A pdb=" N ILE B 392 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLN B 402 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N CYS B 390 " --> pdb=" O GLN B 402 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 33 removed outlier: 3.911A pdb=" N SER C 29 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 24 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 278 through 283 removed outlier: 5.930A pdb=" N ILE C 279 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU C 39 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR C 281 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 35 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU C 36 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N CYS C 335 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 38 " --> pdb=" O CYS C 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 146 through 150 removed outlier: 5.674A pdb=" N THR C 45 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 269 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 256 " --> pdb=" O GLN C 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 291 through 295 removed outlier: 3.725A pdb=" N SER C 291 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 309 through 313 removed outlier: 3.678A pdb=" N TRP C 309 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 317 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 373 through 376 removed outlier: 3.618A pdb=" N SER C 408 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 398 through 402 removed outlier: 7.343A pdb=" N ILE C 392 " --> pdb=" O ILE C 400 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AC4, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.803A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AC6, first strand: chain 'L' and resid 18 through 24 removed outlier: 3.727A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 44 through 46 removed outlier: 3.994A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.07: 2774 1.07 - 1.27: 11076 1.27 - 1.47: 4542 1.47 - 1.67: 5470 1.67 - 1.87: 101 Bond restraints: 23963 Sorted by residual: bond pdb=" CA TYR A 409 " pdb=" C TYR A 409 " ideal model delta sigma weight residual 1.523 1.423 0.100 1.24e-02 6.50e+03 6.50e+01 bond pdb=" C LYS B 188 " pdb=" O LYS B 188 " ideal model delta sigma weight residual 1.236 1.146 0.091 1.15e-02 7.56e+03 6.21e+01 bond pdb=" NE2 GLN B 272 " pdb="HE22 GLN B 272 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ALA A 225 " pdb=" H ALA A 225 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N THR B 223 " pdb=" H THR B 223 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 23958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.53: 42923 6.53 - 13.05: 350 13.05 - 19.58: 14 19.58 - 26.10: 1 26.10 - 32.63: 2 Bond angle restraints: 43290 Sorted by residual: angle pdb=" N PRO A 282 " pdb=" CA PRO A 282 " pdb=" CB PRO A 282 " ideal model delta sigma weight residual 103.25 84.97 18.28 1.05e+00 9.07e-01 3.03e+02 angle pdb=" C GLU A 25 " pdb=" CA GLU A 25 " pdb=" CB GLU A 25 " ideal model delta sigma weight residual 110.42 77.79 32.63 1.99e+00 2.53e-01 2.69e+02 angle pdb=" C LYS C 386 " pdb=" CA LYS C 386 " pdb=" CB LYS C 386 " ideal model delta sigma weight residual 110.42 78.27 32.15 1.99e+00 2.53e-01 2.61e+02 angle pdb=" N ASN A 351 " pdb=" CA ASN A 351 " pdb=" C ASN A 351 " ideal model delta sigma weight residual 112.97 99.47 13.50 1.06e+00 8.90e-01 1.62e+02 angle pdb=" C ASN C 172 " pdb=" CA ASN C 172 " pdb=" CB ASN C 172 " ideal model delta sigma weight residual 111.65 129.79 -18.14 1.44e+00 4.82e-01 1.59e+02 ... (remaining 43285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.75: 9937 19.75 - 39.49: 942 39.49 - 59.24: 400 59.24 - 78.99: 130 78.99 - 98.74: 21 Dihedral angle restraints: 11430 sinusoidal: 6384 harmonic: 5046 Sorted by residual: dihedral pdb=" C GLU A 25 " pdb=" N GLU A 25 " pdb=" CA GLU A 25 " pdb=" CB GLU A 25 " ideal model delta harmonic sigma weight residual -122.60 -80.68 -41.92 0 2.50e+00 1.60e-01 2.81e+02 dihedral pdb=" C LYS C 386 " pdb=" N LYS C 386 " pdb=" CA LYS C 386 " pdb=" CB LYS C 386 " ideal model delta harmonic sigma weight residual -122.60 -85.83 -36.77 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" C CYS A 350 " pdb=" N CYS A 350 " pdb=" CA CYS A 350 " pdb=" CB CYS A 350 " ideal model delta harmonic sigma weight residual -122.60 -154.32 31.72 0 2.50e+00 1.60e-01 1.61e+02 ... (remaining 11427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 1908 0.244 - 0.488: 36 0.488 - 0.732: 1 0.732 - 0.976: 0 0.976 - 1.220: 1 Chirality restraints: 1946 Sorted by residual: chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.92e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.18e+01 chirality pdb=" CA CYS A 350 " pdb=" N CYS A 350 " pdb=" C CYS A 350 " pdb=" CB CYS A 350 " both_signs ideal model delta sigma weight residual False 2.51 1.29 1.22 2.00e-01 2.50e+01 3.72e+01 ... (remaining 1943 not shown) Planarity restraints: 3588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 54 " 0.358 9.50e-02 1.11e+02 3.33e-01 2.19e+03 pdb=" NE ARG L 54 " -0.167 2.00e-02 2.50e+03 pdb=" CZ ARG L 54 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG L 54 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG L 54 " 0.058 2.00e-02 2.50e+03 pdb="HH11 ARG L 54 " 0.623 2.00e-02 2.50e+03 pdb="HH12 ARG L 54 " -0.643 2.00e-02 2.50e+03 pdb="HH21 ARG L 54 " 0.190 2.00e-02 2.50e+03 pdb="HH22 ARG L 54 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 33 " -0.473 2.00e-02 2.50e+03 1.61e-01 1.03e+03 pdb=" CG TRP H 33 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP H 33 " 0.130 2.00e-02 2.50e+03 pdb=" CD2 TRP H 33 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP H 33 " 0.158 2.00e-02 2.50e+03 pdb=" CE2 TRP H 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 33 " 0.089 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 33 " -0.096 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 33 " 0.051 2.00e-02 2.50e+03 pdb=" CH2 TRP H 33 " -0.069 2.00e-02 2.50e+03 pdb=" HD1 TRP H 33 " 0.095 2.00e-02 2.50e+03 pdb=" HE1 TRP H 33 " 0.100 2.00e-02 2.50e+03 pdb=" HE3 TRP H 33 " 0.205 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 33 " -0.177 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 33 " 0.113 2.00e-02 2.50e+03 pdb=" HH2 TRP H 33 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.225 2.00e-02 2.50e+03 1.12e-01 4.98e+02 pdb=" CG TRP H 47 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.130 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " -0.149 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.106 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.093 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 TRP H 47 " 0.190 2.00e-02 2.50e+03 pdb=" HE1 TRP H 47 " -0.092 2.00e-02 2.50e+03 pdb=" HE3 TRP H 47 " -0.091 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 47 " 0.113 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 47 " 0.040 2.00e-02 2.50e+03 pdb=" HH2 TRP H 47 " 0.126 2.00e-02 2.50e+03 ... (remaining 3585 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.81: 207 1.81 - 2.51: 16672 2.51 - 3.21: 73402 3.21 - 3.90: 92692 3.90 - 4.60: 142688 Nonbonded interactions: 325661 Sorted by model distance: nonbonded pdb=" H CYS A 292 " pdb=" HH TYR A 385 " model vdw 1.118 2.100 nonbonded pdb=" HB2 CYS A 350 " pdb=" HA ILE A 354 " model vdw 1.204 2.440 nonbonded pdb="HD21 ASN C 172 " pdb="HH21 ARG C 175 " model vdw 1.240 2.100 nonbonded pdb=" H GLU B 56 " pdb=" HG2 GLU B 56 " model vdw 1.241 2.270 nonbonded pdb=" HG SER A 371 " pdb=" HA CYS A 384 " model vdw 1.294 2.270 ... (remaining 325656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 20 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 21 through 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB or name SG or name H or name HA or name \ HB2 or name HB3)) or resid 293 through 300 or (resid 301 and (name N or name CA \ or name C or name O or name CB or name SG or name H or name HA or name HB2 or n \ ame HB3)) or resid 302 through 501)) selection = (chain 'B' and ((resid 20 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 21 through 501)) selection = (chain 'C' and ((resid 20 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 21 through 56 or (resid 57 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or nam \ e H or name HA or name HB2 or name HB3 or name HD21)) or resid 58 through 90 or \ resid 103 through 501)) } 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 group one per residue 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: 3.050 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: 0.150 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.550 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.011 0.272 12152 Z= 0.646 Angle : 1.886 58.721 16498 Z= 1.101 Chirality : 0.085 1.220 1946 Planarity : 0.017 0.387 2096 Dihedral : 15.095 98.737 4572 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 2.22 % Allowed : 7.71 % Favored : 90.07 % Rotamer: Outliers : 5.63 % Allowed : 3.65 % Favored : 90.72 % Cbeta Deviations : 2.44 % Peptide Plane: Cis-proline : 1.92 % 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 aren not related in a simple way. whole: -1.00 (0.22), residues: 1531 helix: 1.38 (0.27), residues: 393 sheet: -0.37 (0.27), residues: 390 loop : -2.02 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.154 0.009 TYR L 32 PHE 0.124 0.005 PHE H 98 TRP 0.289 0.031 TRP H 33 HIS 0.004 0.001 HIS L 27D Details of bonding type rmsd covalent geometry : bond 0.00879 (12121) covalent geometry : angle 1.57578 (16428) SS BOND : bond 0.15371 ( 23) SS BOND : angle 19.50417 ( 46) hydrogen bonds : bond 0.19734 ( 507) hydrogen bonds : angle 8.06920 ( 1329) link_BETA1-4 : bond 0.02314 ( 3) link_BETA1-4 : angle 4.05801 ( 9) link_NAG-ASN : bond 0.02248 ( 5) link_NAG-ASN : angle 3.95519 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 130 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8218 (mmt) cc_final: 0.7968 (mmm) REVERT: C 171 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8823 (mmtm) REVERT: C 189 MET cc_start: 0.7778 (mmt) cc_final: 0.7545 (mmt) REVERT: C 231 ILE cc_start: 0.9215 (mm) cc_final: 0.8772 (tp) REVERT: C 385 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7872 (m-80) outliers start: 74 outliers final: 49 residues processed: 197 average time/residue: 0.2039 time to fit residues: 60.2318 Evaluate side-chains 144 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 93 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN B 468 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.095065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082479 restraints weight = 104339.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.086106 restraints weight = 46644.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.088517 restraints weight = 25820.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.090105 restraints weight = 16314.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.091172 restraints weight = 11297.262| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12152 Z= 0.184 Angle : 0.740 7.554 16498 Z= 0.394 Chirality : 0.047 0.213 1946 Planarity : 0.005 0.078 2096 Dihedral : 8.244 77.386 1832 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.05 % Favored : 92.29 % Rotamer: Outliers : 0.15 % Allowed : 2.66 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 aren not related in a simple way. whole: -1.01 (0.21), residues: 1531 helix: 1.45 (0.27), residues: 399 sheet: -0.72 (0.25), residues: 429 loop : -1.92 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 90 TYR 0.048 0.002 TYR H 52 PHE 0.034 0.002 PHE H 98 TRP 0.018 0.002 TRP H 33 HIS 0.006 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00412 (12121) covalent geometry : angle 0.72120 (16428) SS BOND : bond 0.00855 ( 23) SS BOND : angle 2.52666 ( 46) hydrogen bonds : bond 0.05044 ( 507) hydrogen bonds : angle 6.55384 ( 1329) link_BETA1-4 : bond 0.00587 ( 3) link_BETA1-4 : angle 3.07569 ( 9) link_NAG-ASN : bond 0.00560 ( 5) link_NAG-ASN : angle 2.65713 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8203 (mmt) cc_final: 0.7979 (mmt) REVERT: C 189 MET cc_start: 0.7833 (mmt) cc_final: 0.7607 (mmt) REVERT: C 231 ILE cc_start: 0.9273 (mm) cc_final: 0.8895 (tp) REVERT: L 89 MET cc_start: 0.6813 (ttp) cc_final: 0.6588 (ttp) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.1852 time to fit residues: 36.2822 Evaluate side-chains 89 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 21 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.093216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080571 restraints weight = 105030.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.084123 restraints weight = 47856.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.086513 restraints weight = 26942.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.088090 restraints weight = 17223.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.089125 restraints weight = 12052.736| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12152 Z= 0.185 Angle : 0.644 6.737 16498 Z= 0.346 Chirality : 0.045 0.216 1946 Planarity : 0.005 0.053 2096 Dihedral : 7.388 62.568 1832 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.90 % Favored : 91.64 % Rotamer: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.20 (0.21), residues: 1531 helix: 1.35 (0.27), residues: 400 sheet: -0.93 (0.25), residues: 420 loop : -2.01 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.027 0.002 TYR H 52 PHE 0.020 0.001 PHE H 98 TRP 0.015 0.002 TRP H 99 HIS 0.004 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00395 (12121) covalent geometry : angle 0.63073 (16428) SS BOND : bond 0.00712 ( 23) SS BOND : angle 1.96527 ( 46) hydrogen bonds : bond 0.04460 ( 507) hydrogen bonds : angle 6.22466 ( 1329) link_BETA1-4 : bond 0.00841 ( 3) link_BETA1-4 : angle 2.61612 ( 9) link_NAG-ASN : bond 0.00392 ( 5) link_NAG-ASN : angle 2.05485 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.7993 (tpt) cc_final: 0.7772 (tpt) REVERT: A 422 ASN cc_start: 0.8411 (t0) cc_final: 0.7985 (t0) REVERT: C 189 MET cc_start: 0.7917 (mmt) cc_final: 0.7673 (mmt) REVERT: C 231 ILE cc_start: 0.9319 (mm) cc_final: 0.8984 (tp) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.2161 time to fit residues: 37.4014 Evaluate side-chains 88 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 5 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN C 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.091590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.078546 restraints weight = 105936.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.082122 restraints weight = 48557.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.084521 restraints weight = 27501.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.086121 restraints weight = 17753.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.087197 restraints weight = 12555.912| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12152 Z= 0.220 Angle : 0.641 6.760 16498 Z= 0.344 Chirality : 0.045 0.203 1946 Planarity : 0.005 0.060 2096 Dihedral : 7.222 59.896 1832 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.36 % Favored : 91.18 % Rotamer: Outliers : 0.08 % Allowed : 2.05 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.42 (0.21), residues: 1531 helix: 1.17 (0.26), residues: 400 sheet: -1.13 (0.25), residues: 424 loop : -2.09 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.022 0.002 TYR L 36 PHE 0.030 0.002 PHE H 98 TRP 0.016 0.002 TRP H 99 HIS 0.003 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00471 (12121) covalent geometry : angle 0.62707 (16428) SS BOND : bond 0.00569 ( 23) SS BOND : angle 2.17081 ( 46) hydrogen bonds : bond 0.04223 ( 507) hydrogen bonds : angle 6.05810 ( 1329) link_BETA1-4 : bond 0.00983 ( 3) link_BETA1-4 : angle 2.38607 ( 9) link_NAG-ASN : bond 0.00278 ( 5) link_NAG-ASN : angle 1.91727 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ASN cc_start: 0.8482 (t0) cc_final: 0.8068 (t0) REVERT: B 189 MET cc_start: 0.8146 (mmp) cc_final: 0.7770 (mmp) REVERT: B 244 MET cc_start: 0.8503 (ttp) cc_final: 0.8231 (ttp) REVERT: B 462 GLN cc_start: 0.8401 (mp10) cc_final: 0.8163 (mp10) REVERT: C 189 MET cc_start: 0.7935 (mmt) cc_final: 0.7684 (mmt) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.1614 time to fit residues: 26.8887 Evaluate side-chains 83 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 103 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.093564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080871 restraints weight = 103942.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.084445 restraints weight = 47186.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.086846 restraints weight = 26325.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.088432 restraints weight = 16751.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.089485 restraints weight = 11669.991| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12152 Z= 0.122 Angle : 0.584 7.070 16498 Z= 0.311 Chirality : 0.044 0.192 1946 Planarity : 0.004 0.049 2096 Dihedral : 6.588 56.040 1832 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.92 % Favored : 92.62 % Rotamer: Outliers : 0.08 % Allowed : 1.90 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.18 (0.21), residues: 1531 helix: 1.48 (0.27), residues: 400 sheet: -1.02 (0.25), residues: 419 loop : -2.00 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.041 0.002 TYR H 52 PHE 0.026 0.001 PHE H 98 TRP 0.014 0.001 TRP H 99 HIS 0.002 0.000 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00264 (12121) covalent geometry : angle 0.57551 (16428) SS BOND : bond 0.00457 ( 23) SS BOND : angle 1.51074 ( 46) hydrogen bonds : bond 0.03794 ( 507) hydrogen bonds : angle 5.73242 ( 1329) link_BETA1-4 : bond 0.00841 ( 3) link_BETA1-4 : angle 2.10517 ( 9) link_NAG-ASN : bond 0.00433 ( 5) link_NAG-ASN : angle 1.70948 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8080 (mt) cc_final: 0.7749 (tt) REVERT: A 422 ASN cc_start: 0.8397 (t0) cc_final: 0.7983 (t0) REVERT: B 462 GLN cc_start: 0.8371 (mp10) cc_final: 0.8135 (mp10) REVERT: C 133 GLU cc_start: 0.7963 (mp0) cc_final: 0.7441 (mp0) REVERT: C 189 MET cc_start: 0.7883 (mmt) cc_final: 0.7609 (mmt) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.2060 time to fit residues: 36.9777 Evaluate side-chains 86 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 115 optimal weight: 0.0470 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.092987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.080419 restraints weight = 105032.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083938 restraints weight = 47756.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.086302 restraints weight = 26793.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.087857 restraints weight = 17098.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.088883 restraints weight = 11969.341| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12152 Z= 0.146 Angle : 0.575 6.541 16498 Z= 0.305 Chirality : 0.044 0.185 1946 Planarity : 0.004 0.072 2096 Dihedral : 6.200 56.509 1832 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.25 % Favored : 92.29 % Rotamer: Outliers : 0.08 % Allowed : 0.99 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.21 (0.21), residues: 1531 helix: 1.50 (0.27), residues: 400 sheet: -1.11 (0.24), residues: 432 loop : -1.99 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 94 TYR 0.016 0.002 TYR L 36 PHE 0.025 0.001 PHE H 98 TRP 0.015 0.002 TRP H 99 HIS 0.002 0.000 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00317 (12121) covalent geometry : angle 0.56467 (16428) SS BOND : bond 0.00463 ( 23) SS BOND : angle 1.70245 ( 46) hydrogen bonds : bond 0.03649 ( 507) hydrogen bonds : angle 5.64192 ( 1329) link_BETA1-4 : bond 0.00763 ( 3) link_BETA1-4 : angle 2.14479 ( 9) link_NAG-ASN : bond 0.00295 ( 5) link_NAG-ASN : angle 1.68474 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8128 (mt) cc_final: 0.7758 (tt) REVERT: A 422 ASN cc_start: 0.8413 (t0) cc_final: 0.8010 (t0) REVERT: C 133 GLU cc_start: 0.8069 (mp0) cc_final: 0.7789 (mp0) REVERT: C 189 MET cc_start: 0.7957 (mmt) cc_final: 0.7677 (mmt) outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.2135 time to fit residues: 36.5597 Evaluate side-chains 86 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.091230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.078468 restraints weight = 105572.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.081988 restraints weight = 48346.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.084346 restraints weight = 27138.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.085927 restraints weight = 17473.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.086969 restraints weight = 12288.300| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12152 Z= 0.219 Angle : 0.623 7.933 16498 Z= 0.333 Chirality : 0.044 0.201 1946 Planarity : 0.005 0.046 2096 Dihedral : 6.238 55.201 1832 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.69 % Favored : 90.86 % Rotamer: Outliers : 0.08 % Allowed : 1.22 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -1.49 (0.21), residues: 1531 helix: 1.18 (0.27), residues: 400 sheet: -1.28 (0.24), residues: 437 loop : -2.11 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.023 0.002 TYR L 36 PHE 0.032 0.002 PHE B 193 TRP 0.020 0.002 TRP H 47 HIS 0.002 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00470 (12121) covalent geometry : angle 0.61028 (16428) SS BOND : bond 0.00532 ( 23) SS BOND : angle 2.02544 ( 46) hydrogen bonds : bond 0.03907 ( 507) hydrogen bonds : angle 5.79042 ( 1329) link_BETA1-4 : bond 0.00885 ( 3) link_BETA1-4 : angle 2.15932 ( 9) link_NAG-ASN : bond 0.00212 ( 5) link_NAG-ASN : angle 1.79777 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8213 (mt) cc_final: 0.7869 (tt) REVERT: B 462 GLN cc_start: 0.8485 (mp10) cc_final: 0.8240 (mp10) REVERT: C 133 GLU cc_start: 0.8010 (mp0) cc_final: 0.7709 (mp0) REVERT: C 189 MET cc_start: 0.7969 (mmt) cc_final: 0.7709 (mmt) outliers start: 1 outliers final: 1 residues processed: 105 average time/residue: 0.2075 time to fit residues: 34.5049 Evaluate side-chains 83 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 39 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.092988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.080376 restraints weight = 103843.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.083958 restraints weight = 46766.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.086371 restraints weight = 25982.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.087934 restraints weight = 16390.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.088954 restraints weight = 11381.338| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12152 Z= 0.118 Angle : 0.555 6.456 16498 Z= 0.294 Chirality : 0.044 0.191 1946 Planarity : 0.004 0.042 2096 Dihedral : 5.838 52.284 1832 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.79 % Favored : 92.75 % Rotamer: Outliers : 0.08 % Allowed : 0.61 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.20 (0.21), residues: 1531 helix: 1.56 (0.27), residues: 399 sheet: -1.10 (0.24), residues: 429 loop : -2.02 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.017 0.001 TYR L 86 PHE 0.029 0.001 PHE H 98 TRP 0.014 0.001 TRP H 99 HIS 0.001 0.000 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00256 (12121) covalent geometry : angle 0.54648 (16428) SS BOND : bond 0.00386 ( 23) SS BOND : angle 1.52126 ( 46) hydrogen bonds : bond 0.03445 ( 507) hydrogen bonds : angle 5.47214 ( 1329) link_BETA1-4 : bond 0.00735 ( 3) link_BETA1-4 : angle 1.68268 ( 9) link_NAG-ASN : bond 0.00377 ( 5) link_NAG-ASN : angle 1.57946 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8228 (mt) cc_final: 0.7860 (tt) REVERT: C 133 GLU cc_start: 0.8111 (mp0) cc_final: 0.7857 (mp0) REVERT: C 189 MET cc_start: 0.7866 (mmt) cc_final: 0.7566 (mmt) REVERT: C 280 ASP cc_start: 0.8527 (m-30) cc_final: 0.7973 (t0) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.2196 time to fit residues: 36.3956 Evaluate side-chains 86 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 129 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 = 0.3665 r_free = 0.3665 target = 0.091700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.079422 restraints weight = 107202.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.082860 restraints weight = 48889.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.085161 restraints weight = 27405.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.086669 restraints weight = 17495.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.087671 restraints weight = 12263.938| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12152 Z= 0.172 Angle : 0.582 7.402 16498 Z= 0.309 Chirality : 0.044 0.194 1946 Planarity : 0.004 0.048 2096 Dihedral : 5.888 54.652 1832 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.56 % Favored : 91.05 % Rotamer: Outliers : 0.08 % Allowed : 0.46 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.34 (0.21), residues: 1531 helix: 1.44 (0.27), residues: 399 sheet: -1.16 (0.24), residues: 430 loop : -2.11 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.020 0.002 TYR B 310 PHE 0.033 0.002 PHE H 98 TRP 0.016 0.002 TRP H 99 HIS 0.002 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00371 (12121) covalent geometry : angle 0.57501 (16428) SS BOND : bond 0.00507 ( 23) SS BOND : angle 1.35461 ( 46) hydrogen bonds : bond 0.03610 ( 507) hydrogen bonds : angle 5.54188 ( 1329) link_BETA1-4 : bond 0.00617 ( 3) link_BETA1-4 : angle 1.56707 ( 9) link_NAG-ASN : bond 0.00187 ( 5) link_NAG-ASN : angle 1.68402 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8270 (mt) cc_final: 0.7929 (tt) REVERT: C 133 GLU cc_start: 0.7885 (mp0) cc_final: 0.7647 (mp0) REVERT: C 280 ASP cc_start: 0.8525 (m-30) cc_final: 0.8026 (t0) outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.2178 time to fit residues: 34.9501 Evaluate side-chains 82 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 131 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.092969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.080594 restraints weight = 107196.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.084083 restraints weight = 48863.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.086419 restraints weight = 27339.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.087949 restraints weight = 17394.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.088989 restraints weight = 12155.384| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12152 Z= 0.123 Angle : 0.552 6.534 16498 Z= 0.292 Chirality : 0.044 0.182 1946 Planarity : 0.004 0.044 2096 Dihedral : 5.721 52.748 1832 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.58 % Favored : 92.03 % Rotamer: Outliers : 0.08 % Allowed : 0.30 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.15 (0.22), residues: 1531 helix: 1.59 (0.27), residues: 399 sheet: -0.99 (0.24), residues: 422 loop : -2.04 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.018 0.001 TYR B 299 PHE 0.032 0.001 PHE H 98 TRP 0.015 0.001 TRP H 99 HIS 0.004 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00268 (12121) covalent geometry : angle 0.54696 (16428) SS BOND : bond 0.00336 ( 23) SS BOND : angle 1.17312 ( 46) hydrogen bonds : bond 0.03400 ( 507) hydrogen bonds : angle 5.41266 ( 1329) link_BETA1-4 : bond 0.00645 ( 3) link_BETA1-4 : angle 1.31441 ( 9) link_NAG-ASN : bond 0.00291 ( 5) link_NAG-ASN : angle 1.54827 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8239 (mt) cc_final: 0.7888 (tt) REVERT: A 422 ASN cc_start: 0.8427 (t0) cc_final: 0.8036 (t0) REVERT: B 250 MET cc_start: 0.8137 (mmm) cc_final: 0.7653 (mmm) REVERT: C 133 GLU cc_start: 0.7899 (mp0) cc_final: 0.7678 (mp0) REVERT: C 280 ASP cc_start: 0.8558 (m-30) cc_final: 0.8063 (t0) outliers start: 1 outliers final: 1 residues processed: 103 average time/residue: 0.2114 time to fit residues: 34.2207 Evaluate side-chains 81 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.092148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.079597 restraints weight = 106195.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.083145 restraints weight = 47835.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.085507 restraints weight = 26594.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.087074 restraints weight = 16868.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.088109 restraints weight = 11727.265| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12152 Z= 0.155 Angle : 0.567 6.488 16498 Z= 0.302 Chirality : 0.043 0.189 1946 Planarity : 0.004 0.047 2096 Dihedral : 5.681 53.371 1832 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.49 % Favored : 91.12 % Rotamer: Outliers : 0.08 % Allowed : 0.15 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -1.21 (0.21), residues: 1531 helix: 1.50 (0.27), residues: 399 sheet: -0.99 (0.25), residues: 420 loop : -2.07 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 27C TYR 0.015 0.002 TYR B 310 PHE 0.037 0.002 PHE H 98 TRP 0.015 0.002 TRP H 99 HIS 0.001 0.001 HIS B 332 Details of bonding type rmsd covalent geometry : bond 0.00336 (12121) covalent geometry : angle 0.56020 (16428) SS BOND : bond 0.00397 ( 23) SS BOND : angle 1.34869 ( 46) hydrogen bonds : bond 0.03474 ( 507) hydrogen bonds : angle 5.45961 ( 1329) link_BETA1-4 : bond 0.00655 ( 3) link_BETA1-4 : angle 1.36867 ( 9) link_NAG-ASN : bond 0.00179 ( 5) link_NAG-ASN : angle 1.61756 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.06 seconds wall clock time: 54 minutes 16.73 seconds (3256.73 seconds total)