Starting phenix.real_space_refine on Thu Jul 2 18:37:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d7r_27231/07_2026/8d7r_27231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7r_27231/07_2026/8d7r_27231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2026/8d7r_27231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2026/8d7r_27231.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2026/8d7r_27231.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2026/8d7r_27231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2026/8d7r_27231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7r_27231/07_2026/8d7r_27231.map" } resolution = 3.9 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 6158 2.51 5 N 1608 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9627 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} Chain: "C" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1607 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 20, 'TRANS': 178} Chain: "B" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3197 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 378} Chain breaks: 1 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3167 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 25, 'TRANS': 366} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.01, per 1000 atoms: 0.21 Number of scatterers: 9627 At special positions: 0 Unit cell: (102.34, 144.48, 151.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1825 8.00 N 1608 7.00 C 6158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.04 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 466 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 701 " - " ASN A 131 " " NAG A 702 " - " ASN A 157 " " NAG A 703 " - " ASN A 383 " " NAG A 704 " - " ASN A 379 " " NAG B 901 " - " ASN B 426 " " NAG C 401 " - " ASN C 142 " " NAG E 1 " - " ASN C 190 " " NAG F 1 " - " ASN B 407 " " NAG G 1 " - " ASN B 303 " " NAG H 1 " - " ASN B 243 " " NAG I 1 " - " ASN A 227 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 337.7 milliseconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 21 sheets defined 12.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'D' and resid 35 through 65 removed outlier: 3.987A pdb=" N SER D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 71 removed outlier: 3.699A pdb=" N ASN D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 66 through 71' Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.969A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 124 Processing helix chain 'D' and resid 126 through 154 Processing helix chain 'D' and resid 176 through 210 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 355 through 360 Processing sheet with id=AA1, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AA2, first strand: chain 'C' and resid 211 through 214 Processing sheet with id=AA3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 147 removed outlier: 3.875A pdb=" N ASN B 143 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 156 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 152 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP B 157 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS B 201 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.565A pdb=" N ASN B 191 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG B 221 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 175 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 219 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 177 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 244 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 242 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.720A pdb=" N ILE B 267 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 301 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 269 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 297 " --> pdb=" O CYS B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.652A pdb=" N ILE B 261 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 330 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 323 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 315 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 280 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 317 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 342 removed outlier: 5.712A pdb=" N GLN B 338 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN B 354 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN B 340 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 352 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.844A pdb=" N VAL B 380 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 371 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 409 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR B 406 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 425 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 421 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 419 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 477 through 481 removed outlier: 3.688A pdb=" N ARG B 510 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 469 " --> pdb=" O ARG B 508 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 508 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 471 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 137 removed outlier: 7.684A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.613A pdb=" N LYS A 161 " --> pdb=" O TRP A 197 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.613A pdb=" N LYS A 161 " --> pdb=" O TRP A 197 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 194 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 214 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 196 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 212 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.527A pdb=" N ASN A 227 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 245 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 229 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 243 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 231 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS A 241 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.781A pdb=" N MET A 302 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 258 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG A 300 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 260 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 298 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 262 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 296 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.905A pdb=" N VAL A 347 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 389 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 349 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.748A pdb=" N GLN A 378 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 403 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 397 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 396 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AC2, first strand: chain 'A' and resid 459 through 460 removed outlier: 4.019A pdb=" N CYS A 491 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 469 through 474 removed outlier: 3.568A pdb=" N ASP A 469 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 471 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 455 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 499 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR A 492 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 512 " --> pdb=" O TYR A 492 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3010 1.34 - 1.46: 2438 1.46 - 1.58: 4403 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 9899 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 9894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 13120 1.41 - 2.82: 318 2.82 - 4.23: 53 4.23 - 5.63: 10 5.63 - 7.04: 7 Bond angle restraints: 13508 Sorted by residual: angle pdb=" C PRO A 434 " pdb=" N LYS A 435 " pdb=" CA LYS A 435 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C ALA B 448 " pdb=" N VAL B 449 " pdb=" CA VAL B 449 " ideal model delta sigma weight residual 120.49 125.19 -4.70 1.38e+00 5.25e-01 1.16e+01 angle pdb=" N ASN A 131 " pdb=" CA ASN A 131 " pdb=" CB ASN A 131 " ideal model delta sigma weight residual 114.17 110.31 3.86 1.14e+00 7.69e-01 1.15e+01 angle pdb=" CA GLY A 361 " pdb=" C GLY A 361 " pdb=" N LYS A 362 " ideal model delta sigma weight residual 114.23 116.74 -2.51 8.80e-01 1.29e+00 8.14e+00 angle pdb=" C LEU B 194 " pdb=" N ASN B 195 " pdb=" CA ASN B 195 " ideal model delta sigma weight residual 121.54 126.97 -5.43 1.91e+00 2.74e-01 8.08e+00 ... (remaining 13503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5354 17.79 - 35.59: 364 35.59 - 53.38: 58 53.38 - 71.17: 8 71.17 - 88.97: 9 Dihedral angle restraints: 5793 sinusoidal: 2346 harmonic: 3447 Sorted by residual: dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual 93.00 173.22 -80.22 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS A 458 " pdb=" SG CYS A 458 " pdb=" SG CYS A 466 " pdb=" CB CYS A 466 " ideal model delta sinusoidal sigma weight residual -86.00 -34.89 -51.11 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CB CYS C 116 " pdb=" SG CYS C 116 " pdb=" SG CYS C 127 " pdb=" CB CYS C 127 " ideal model delta sinusoidal sigma weight residual 93.00 60.67 32.33 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 5790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1270 0.049 - 0.098: 198 0.098 - 0.147: 76 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1547 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 190 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 131 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 383 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1544 not shown) Planarity restraints: 1696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 66 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO D 67 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 500 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 501 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 272 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 273 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " 0.022 5.00e-02 4.00e+02 ... (remaining 1693 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3184 2.86 - 3.37: 8390 3.37 - 3.88: 14623 3.88 - 4.39: 15262 4.39 - 4.90: 26904 Nonbonded interactions: 68363 Sorted by model distance: nonbonded pdb=" NH1 ARG A 262 " pdb=" O THR A 263 " model vdw 2.345 3.120 nonbonded pdb=" O GLU D 92 " pdb=" OG SER D 96 " model vdw 2.348 3.040 nonbonded pdb=" O TYR A 257 " pdb=" OG1 THR A 277 " model vdw 2.370 3.040 nonbonded pdb=" OG SER B 374 " pdb=" O5 NAG F 1 " model vdw 2.375 3.040 nonbonded pdb=" OE1 GLU B 373 " pdb=" N SER B 376 " model vdw 2.380 3.120 ... (remaining 68358 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.670 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9923 Z= 0.137 Angle : 0.548 7.773 13572 Z= 0.273 Chirality : 0.042 0.245 1547 Planarity : 0.004 0.056 1685 Dihedral : 11.987 88.966 3529 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.21), residues: 1157 helix: 1.59 (0.42), residues: 129 sheet: -1.70 (0.28), residues: 305 loop : -3.30 (0.17), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 167 TYR 0.011 0.001 TYR B 502 PHE 0.013 0.000 PHE A 332 TRP 0.004 0.000 TRP A 146 HIS 0.001 0.000 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 9899) covalent geometry : angle 0.53647 / 0.27 (13508) SS BOND : bond 0.00222 / 0.15 ( 8) SS BOND : angle 0.46437 / 0.29 ( 16) hydrogen bonds : bond 0.23422 / 16.43 ( 211) hydrogen bonds : angle 8.05712 / 5.53 ( 585) link_BETA1-4 : bond 0.00317 / 0.19 ( 5) link_BETA1-4 : angle 1.49354 / 0.98 ( 15) link_NAG-ASN : bond 0.00422 / 0.24 ( 11) link_NAG-ASN : angle 2.11636 / 1.63 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 MET cc_start: 0.5426 (ptp) cc_final: 0.4966 (mpp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1175 time to fit residues: 28.9256 Evaluate side-chains 99 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 105 GLN D 112 HIS D 123 GLN D 135 HIS D 192 GLN C 162 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN B 190 HIS B 201 HIS B 226 ASN B 286 ASN B 402 ASN B 420 GLN B 434 HIS A 287 GLN A 348 GLN A 478 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.192607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.171046 restraints weight = 19216.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.170027 restraints weight = 25345.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171687 restraints weight = 20497.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171757 restraints weight = 14070.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.171789 restraints weight = 14915.002| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 9923 Z= 0.136 Angle : 0.654 10.424 13572 Z= 0.316 Chirality : 0.047 0.547 1547 Planarity : 0.004 0.046 1685 Dihedral : 3.682 29.164 1256 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.70 % Allowed : 12.67 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.23), residues: 1157 helix: 2.25 (0.45), residues: 135 sheet: -1.55 (0.26), residues: 350 loop : -2.84 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 78 TYR 0.023 0.001 TYR B 502 PHE 0.017 0.001 PHE C 141 TRP 0.021 0.001 TRP A 457 HIS 0.008 0.001 HIS C 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9899) covalent geometry : angle 0.63424 / 0.31 (13508) SS BOND : bond 0.00386 / 0.23 ( 8) SS BOND : angle 2.00822 / 0.83 ( 16) hydrogen bonds : bond 0.04630 / 3.16 ( 211) hydrogen bonds : angle 5.93027 / 4.11 ( 585) link_BETA1-4 : bond 0.00553 / 0.33 ( 5) link_BETA1-4 : angle 1.42484 / 0.90 ( 15) link_NAG-ASN : bond 0.01137 / 0.74 ( 11) link_NAG-ASN : angle 2.87340 / 2.18 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 103 LEU cc_start: 0.4513 (mm) cc_final: 0.4268 (mt) REVERT: D 182 MET cc_start: 0.6566 (mmm) cc_final: 0.6238 (mmp) REVERT: C 142 ASN cc_start: 0.4724 (OUTLIER) cc_final: 0.4148 (m110) REVERT: B 438 SER cc_start: 0.7460 (p) cc_final: 0.7216 (m) REVERT: A 438 MET cc_start: 0.5557 (ptp) cc_final: 0.5221 (mpp) outliers start: 18 outliers final: 10 residues processed: 124 average time/residue: 0.1159 time to fit residues: 19.4275 Evaluate side-chains 93 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 406 TYR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 478 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 0.0040 chunk 41 optimal weight: 0.9980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS B 434 HIS B 527 GLN A 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.186917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.166883 restraints weight = 18998.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.166602 restraints weight = 25213.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.168025 restraints weight = 20525.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.167639 restraints weight = 14778.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.168016 restraints weight = 15165.456| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9923 Z= 0.130 Angle : 0.641 9.775 13572 Z= 0.309 Chirality : 0.045 0.458 1547 Planarity : 0.004 0.042 1685 Dihedral : 3.828 20.461 1256 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.17 % Allowed : 14.37 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.23), residues: 1157 helix: 2.62 (0.47), residues: 135 sheet: -1.43 (0.26), residues: 355 loop : -2.59 (0.21), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 176 TYR 0.013 0.001 TYR D 49 PHE 0.019 0.001 PHE A 332 TRP 0.029 0.001 TRP B 246 HIS 0.014 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9899) covalent geometry : angle 0.61849 / 0.30 (13508) SS BOND : bond 0.00855 / 0.45 ( 8) SS BOND : angle 2.01339 / 0.85 ( 16) hydrogen bonds : bond 0.04842 / 3.28 ( 211) hydrogen bonds : angle 5.41825 / 3.78 ( 585) link_BETA1-4 : bond 0.00362 / 0.22 ( 5) link_BETA1-4 : angle 1.49090 / 0.97 ( 15) link_NAG-ASN : bond 0.00378 / 0.22 ( 11) link_NAG-ASN : angle 3.11009 / 2.21 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 182 MET cc_start: 0.6958 (mmm) cc_final: 0.6677 (mmp) REVERT: C 245 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7070 (ptm160) REVERT: C 252 ASP cc_start: 0.6316 (OUTLIER) cc_final: 0.5983 (t0) REVERT: C 275 GLU cc_start: 0.5396 (mm-30) cc_final: 0.5118 (tm-30) REVERT: B 438 SER cc_start: 0.7283 (p) cc_final: 0.6973 (m) REVERT: A 438 MET cc_start: 0.5509 (ptp) cc_final: 0.5237 (mpp) outliers start: 23 outliers final: 14 residues processed: 118 average time/residue: 0.0989 time to fit residues: 16.4126 Evaluate side-chains 107 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 341 CYS Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 6.9990 chunk 5 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 HIS B 477 GLN B 527 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.182653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.160768 restraints weight = 19209.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.159987 restraints weight = 26231.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.161537 restraints weight = 21252.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.161477 restraints weight = 15161.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.161585 restraints weight = 13605.863| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9923 Z= 0.136 Angle : 0.639 8.755 13572 Z= 0.307 Chirality : 0.045 0.455 1547 Planarity : 0.004 0.045 1685 Dihedral : 4.011 20.554 1256 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.31 % Allowed : 15.60 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.24), residues: 1157 helix: 3.15 (0.48), residues: 129 sheet: -1.28 (0.26), residues: 365 loop : -2.47 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.024 0.002 TYR B 502 PHE 0.013 0.001 PHE A 332 TRP 0.009 0.001 TRP C 232 HIS 0.020 0.001 HIS A 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9899) covalent geometry : angle 0.62188 / 0.30 (13508) SS BOND : bond 0.00599 / 0.35 ( 8) SS BOND : angle 1.84680 / 0.81 ( 16) hydrogen bonds : bond 0.05065 / 3.39 ( 211) hydrogen bonds : angle 5.11699 / 3.60 ( 585) link_BETA1-4 : bond 0.00417 / 0.25 ( 5) link_BETA1-4 : angle 1.51951 / 1.02 ( 15) link_NAG-ASN : bond 0.00385 / 0.21 ( 11) link_NAG-ASN : angle 2.65932 / 1.89 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8538 (tp) REVERT: D 133 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7119 (tp) REVERT: C 245 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7153 (ptm160) REVERT: C 252 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5903 (t0) REVERT: A 313 TRP cc_start: 0.7079 (m100) cc_final: 0.6439 (m100) outliers start: 35 outliers final: 19 residues processed: 131 average time/residue: 0.0920 time to fit residues: 17.3058 Evaluate side-chains 115 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 108 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 180 GLN B 477 GLN B 527 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.183500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.161327 restraints weight = 19176.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.160745 restraints weight = 24580.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.161784 restraints weight = 21114.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.161959 restraints weight = 16285.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.162082 restraints weight = 14687.569| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9923 Z= 0.113 Angle : 0.635 10.571 13572 Z= 0.301 Chirality : 0.044 0.322 1547 Planarity : 0.004 0.042 1685 Dihedral : 3.904 20.297 1256 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.36 % Allowed : 17.67 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.24), residues: 1157 helix: 3.36 (0.47), residues: 129 sheet: -1.05 (0.27), residues: 357 loop : -2.36 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 357 TYR 0.011 0.001 TYR A 295 PHE 0.012 0.001 PHE A 332 TRP 0.026 0.001 TRP A 351 HIS 0.003 0.000 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9899) covalent geometry : angle 0.61428 / 0.30 (13508) SS BOND : bond 0.00822 / 0.44 ( 8) SS BOND : angle 1.96303 / 0.81 ( 16) hydrogen bonds : bond 0.04632 / 3.13 ( 211) hydrogen bonds : angle 4.86248 / 3.41 ( 585) link_BETA1-4 : bond 0.00447 / 0.27 ( 5) link_BETA1-4 : angle 1.57142 / 1.04 ( 15) link_NAG-ASN : bond 0.00784 / 0.50 ( 11) link_NAG-ASN : angle 2.89709 / 2.02 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8793 (tp) cc_final: 0.8483 (tp) REVERT: D 133 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7112 (tp) REVERT: C 275 GLU cc_start: 0.5552 (mm-30) cc_final: 0.5190 (tm-30) REVERT: A 313 TRP cc_start: 0.7017 (m100) cc_final: 0.6547 (m100) REVERT: A 478 HIS cc_start: 0.5652 (OUTLIER) cc_final: 0.5384 (t-170) outliers start: 25 outliers final: 14 residues processed: 121 average time/residue: 0.1016 time to fit residues: 17.1245 Evaluate side-chains 113 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 478 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 5 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 98 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 434 HIS B 527 GLN A 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.183515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.161939 restraints weight = 19103.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.161234 restraints weight = 26992.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.162429 restraints weight = 23353.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.162867 restraints weight = 16853.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.162872 restraints weight = 14905.596| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9923 Z= 0.112 Angle : 0.628 11.224 13572 Z= 0.300 Chirality : 0.044 0.350 1547 Planarity : 0.004 0.043 1685 Dihedral : 3.939 23.423 1256 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.65 % Allowed : 18.05 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.24), residues: 1157 helix: 3.40 (0.46), residues: 129 sheet: -0.94 (0.27), residues: 358 loop : -2.24 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 176 TYR 0.034 0.001 TYR D 110 PHE 0.021 0.001 PHE A 332 TRP 0.010 0.001 TRP A 333 HIS 0.003 0.000 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9899) covalent geometry : angle 0.61183 / 0.30 (13508) SS BOND : bond 0.01013 / 0.53 ( 8) SS BOND : angle 1.90402 / 0.79 ( 16) hydrogen bonds : bond 0.04519 / 3.06 ( 211) hydrogen bonds : angle 4.74619 / 3.33 ( 585) link_BETA1-4 : bond 0.00411 / 0.25 ( 5) link_BETA1-4 : angle 1.58829 / 1.05 ( 15) link_NAG-ASN : bond 0.00486 / 0.29 ( 11) link_NAG-ASN : angle 2.43825 / 1.71 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8475 (tp) REVERT: D 133 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7138 (tp) REVERT: C 245 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6964 (ptm160) REVERT: A 332 PHE cc_start: 0.5325 (OUTLIER) cc_final: 0.4685 (t80) REVERT: A 478 HIS cc_start: 0.5642 (OUTLIER) cc_final: 0.5427 (t-170) outliers start: 28 outliers final: 17 residues processed: 127 average time/residue: 0.0877 time to fit residues: 15.5393 Evaluate side-chains 125 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 478 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 110 optimal weight: 0.0370 chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 298 HIS B 454 HIS B 527 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.181670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.160981 restraints weight = 19104.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.160286 restraints weight = 26858.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.161182 restraints weight = 22156.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.161432 restraints weight = 17028.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.161653 restraints weight = 16127.855| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9923 Z= 0.118 Angle : 0.645 12.454 13572 Z= 0.308 Chirality : 0.044 0.295 1547 Planarity : 0.004 0.044 1685 Dihedral : 4.011 21.608 1256 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.02 % Allowed : 18.15 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.24), residues: 1157 helix: 3.40 (0.46), residues: 129 sheet: -0.81 (0.27), residues: 358 loop : -2.15 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 176 TYR 0.026 0.001 TYR D 110 PHE 0.020 0.001 PHE A 332 TRP 0.011 0.001 TRP B 519 HIS 0.003 0.000 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9899) covalent geometry : angle 0.63042 / 0.30 (13508) SS BOND : bond 0.00825 / 0.44 ( 8) SS BOND : angle 1.72154 / 0.74 ( 16) hydrogen bonds : bond 0.04673 / 3.15 ( 211) hydrogen bonds : angle 4.61937 / 3.26 ( 585) link_BETA1-4 : bond 0.00421 / 0.26 ( 5) link_BETA1-4 : angle 1.60191 / 1.06 ( 15) link_NAG-ASN : bond 0.00420 / 0.24 ( 11) link_NAG-ASN : angle 2.37523 / 1.63 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8487 (tp) REVERT: D 113 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8087 (mp) REVERT: D 133 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.6991 (tp) REVERT: C 245 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7038 (ptm160) REVERT: A 313 TRP cc_start: 0.7209 (m100) cc_final: 0.6748 (m100) REVERT: A 328 LYS cc_start: 0.6837 (tmtt) cc_final: 0.6370 (tttm) REVERT: A 332 PHE cc_start: 0.5410 (OUTLIER) cc_final: 0.4757 (t80) outliers start: 32 outliers final: 20 residues processed: 130 average time/residue: 0.1094 time to fit residues: 19.6739 Evaluate side-chains 129 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 0.3980 chunk 79 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 20 optimal weight: 0.1980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 527 GLN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.182805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.162262 restraints weight = 18856.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.161957 restraints weight = 26206.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.163246 restraints weight = 20657.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.163211 restraints weight = 15491.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.163677 restraints weight = 14974.707| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9923 Z= 0.110 Angle : 0.637 11.820 13572 Z= 0.305 Chirality : 0.043 0.289 1547 Planarity : 0.004 0.044 1685 Dihedral : 3.934 21.228 1256 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.55 % Allowed : 19.28 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.25), residues: 1157 helix: 3.47 (0.45), residues: 129 sheet: -0.74 (0.27), residues: 358 loop : -2.08 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 176 TYR 0.025 0.001 TYR D 110 PHE 0.021 0.001 PHE A 332 TRP 0.009 0.001 TRP B 519 HIS 0.003 0.000 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9899) covalent geometry : angle 0.62365 / 0.30 (13508) SS BOND : bond 0.00678 / 0.38 ( 8) SS BOND : angle 1.55734 / 0.68 ( 16) hydrogen bonds : bond 0.04361 / 2.96 ( 211) hydrogen bonds : angle 4.50415 / 3.19 ( 585) link_BETA1-4 : bond 0.00441 / 0.26 ( 5) link_BETA1-4 : angle 1.61689 / 1.06 ( 15) link_NAG-ASN : bond 0.00431 / 0.25 ( 11) link_NAG-ASN : angle 2.35773 / 1.63 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8468 (tp) REVERT: D 113 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8064 (mp) REVERT: D 133 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7208 (tp) REVERT: C 245 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6954 (ptm160) REVERT: B 510 ARG cc_start: 0.3666 (tmm-80) cc_final: 0.3149 (tmm-80) REVERT: A 328 LYS cc_start: 0.6955 (tmtt) cc_final: 0.6496 (tttm) REVERT: A 332 PHE cc_start: 0.5266 (OUTLIER) cc_final: 0.4715 (t80) outliers start: 27 outliers final: 18 residues processed: 124 average time/residue: 0.1085 time to fit residues: 18.6736 Evaluate side-chains 124 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 50.0000 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN ** A 478 HIS ** 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 = 0.4403 r_free = 0.4403 target = 0.173486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.152617 restraints weight = 19200.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.151825 restraints weight = 27052.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.153301 restraints weight = 20575.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.152880 restraints weight = 14914.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.153292 restraints weight = 15137.605| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9923 Z= 0.171 Angle : 0.737 11.317 13572 Z= 0.360 Chirality : 0.046 0.283 1547 Planarity : 0.005 0.055 1685 Dihedral : 4.682 25.725 1256 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.55 % Allowed : 19.47 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.24), residues: 1157 helix: 3.23 (0.46), residues: 126 sheet: -1.06 (0.27), residues: 354 loop : -2.17 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 176 TYR 0.016 0.002 TYR D 110 PHE 0.019 0.002 PHE A 332 TRP 0.023 0.002 TRP C 232 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 9899) covalent geometry : angle 0.72314 / 0.36 (13508) SS BOND : bond 0.00866 / 0.47 ( 8) SS BOND : angle 1.87558 / 0.96 ( 16) hydrogen bonds : bond 0.06437 / 4.28 ( 211) hydrogen bonds : angle 4.84511 / 3.46 ( 585) link_BETA1-4 : bond 0.00379 / 0.23 ( 5) link_BETA1-4 : angle 1.63875 / 1.10 ( 15) link_NAG-ASN : bond 0.00425 / 0.23 ( 11) link_NAG-ASN : angle 2.50641 / 1.67 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8692 (tp) REVERT: D 113 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8211 (mp) REVERT: C 236 GLU cc_start: 0.6122 (mm-30) cc_final: 0.5764 (mm-30) REVERT: B 474 ASN cc_start: 0.6280 (t0) cc_final: 0.5790 (t0) REVERT: A 206 LYS cc_start: 0.4477 (pptt) cc_final: 0.3521 (pptt) REVERT: A 328 LYS cc_start: 0.7025 (tmtt) cc_final: 0.6598 (tttm) REVERT: A 332 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.4728 (t80) outliers start: 27 outliers final: 23 residues processed: 126 average time/residue: 0.1080 time to fit residues: 18.9049 Evaluate side-chains 129 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN A 348 GLN A 472 GLN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.175585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.153474 restraints weight = 18986.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.152533 restraints weight = 24374.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.153697 restraints weight = 20503.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.153880 restraints weight = 15339.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.154134 restraints weight = 14313.877| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9923 Z= 0.133 Angle : 0.690 10.959 13572 Z= 0.335 Chirality : 0.044 0.269 1547 Planarity : 0.005 0.055 1685 Dihedral : 4.456 24.051 1256 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.55 % Allowed : 19.66 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.24), residues: 1157 helix: 3.37 (0.45), residues: 126 sheet: -1.02 (0.27), residues: 354 loop : -2.09 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 176 TYR 0.022 0.001 TYR A 453 PHE 0.019 0.001 PHE A 332 TRP 0.014 0.001 TRP B 519 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9899) covalent geometry : angle 0.67635 / 0.33 (13508) SS BOND : bond 0.00689 / 0.40 ( 8) SS BOND : angle 1.63617 / 0.83 ( 16) hydrogen bonds : bond 0.05593 / 3.73 ( 211) hydrogen bonds : angle 4.73016 / 3.38 ( 585) link_BETA1-4 : bond 0.00435 / 0.27 ( 5) link_BETA1-4 : angle 1.65986 / 1.10 ( 15) link_NAG-ASN : bond 0.00450 / 0.24 ( 11) link_NAG-ASN : angle 2.39531 / 1.64 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8703 (tp) REVERT: D 113 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8128 (mp) REVERT: D 154 LEU cc_start: 0.8641 (mm) cc_final: 0.8381 (mp) REVERT: C 245 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7322 (ptm160) REVERT: B 474 ASN cc_start: 0.6350 (t0) cc_final: 0.5888 (t0) REVERT: A 206 LYS cc_start: 0.4220 (pptt) cc_final: 0.3292 (pptt) REVERT: A 313 TRP cc_start: 0.7429 (m100) cc_final: 0.6942 (m100) REVERT: A 328 LYS cc_start: 0.6950 (tmtt) cc_final: 0.6556 (tttm) REVERT: A 332 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.4973 (t80) REVERT: A 348 GLN cc_start: 0.7156 (tp-100) cc_final: 0.6908 (tt0) outliers start: 27 outliers final: 19 residues processed: 125 average time/residue: 0.1087 time to fit residues: 19.0111 Evaluate side-chains 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.0010 chunk 70 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.176648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.155262 restraints weight = 18761.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.154767 restraints weight = 22997.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.155896 restraints weight = 19324.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.155837 restraints weight = 14980.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.155926 restraints weight = 13704.456| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9923 Z= 0.127 Angle : 0.682 10.608 13572 Z= 0.332 Chirality : 0.044 0.259 1547 Planarity : 0.004 0.055 1685 Dihedral : 4.389 23.619 1256 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.55 % Allowed : 20.13 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.25), residues: 1157 helix: 3.50 (0.45), residues: 126 sheet: -0.98 (0.27), residues: 363 loop : -2.06 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 176 TYR 0.029 0.001 TYR A 322 PHE 0.020 0.001 PHE A 332 TRP 0.010 0.001 TRP C 232 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9899) covalent geometry : angle 0.66977 / 0.33 (13508) SS BOND : bond 0.00703 / 0.40 ( 8) SS BOND : angle 1.42873 / 0.74 ( 16) hydrogen bonds : bond 0.05186 / 3.50 ( 211) hydrogen bonds : angle 4.57845 / 3.27 ( 585) link_BETA1-4 : bond 0.00404 / 0.25 ( 5) link_BETA1-4 : angle 1.65725 / 1.09 ( 15) link_NAG-ASN : bond 0.00445 / 0.24 ( 11) link_NAG-ASN : angle 2.34127 / 1.62 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.03 seconds wall clock time: 30 minutes 25.04 seconds (1825.04 seconds total)