Starting phenix.real_space_refine on Wed Mar 4 01:03:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7r_27231/03_2026/8d7r_27231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7r_27231/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7r_27231/03_2026/8d7r_27231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7r_27231/03_2026/8d7r_27231.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7r_27231/03_2026/8d7r_27231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7r_27231/03_2026/8d7r_27231.cif" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.83, per 1000 atoms: 0.19 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: 0.69 Conformation dependent library (CDL) restraints added in 447.0 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: 1.43 Time building geometry restraints manager: 0.92 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 - 21.88: 5767 21.88 - 43.76: 270 43.76 - 65.64: 57 65.64 - 87.52: 9 87.52 - 109.39: 26 Dihedral angle restraints: 6129 sinusoidal: 2682 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 6126 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: 4.470 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 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 : 15.026 109.395 3865 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 covalent geometry : bond 0.00276 ( 9899) covalent geometry : angle 0.53647 (13508) SS BOND : bond 0.00222 ( 8) SS BOND : angle 0.46437 ( 16) hydrogen bonds : bond 0.23422 ( 211) hydrogen bonds : angle 8.05712 ( 585) link_BETA1-4 : bond 0.00317 ( 5) link_BETA1-4 : angle 1.49354 ( 15) link_NAG-ASN : bond 0.00422 ( 11) link_NAG-ASN : angle 2.11636 ( 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 : 0.346 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: 0.1131 time to fit residues: 27.7697 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 : 0.360 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 434 HIS A 287 GLN A 348 GLN A 478 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.193472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.173235 restraints weight = 19278.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.172774 restraints weight = 24377.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.174098 restraints weight = 18611.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.174165 restraints weight = 14296.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.174097 restraints weight = 13584.621| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.1975 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= 0.134 Angle : 0.668 15.397 13572 Z= 0.318 Chirality : 0.051 0.904 1547 Planarity : 0.004 0.046 1685 Dihedral : 12.457 92.477 1592 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.32 % Allowed : 12.48 % Favored : 86.20 % 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: -2.63 (0.23), residues: 1157 helix: 2.26 (0.45), residues: 135 sheet: -1.48 (0.27), residues: 347 loop : -2.90 (0.20), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 262 TYR 0.020 0.001 TYR B 502 PHE 0.018 0.001 PHE C 141 TRP 0.022 0.001 TRP A 457 HIS 0.008 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9899) covalent geometry : angle 0.63831 (13508) SS BOND : bond 0.00440 ( 8) SS BOND : angle 2.09212 ( 16) hydrogen bonds : bond 0.04825 ( 211) hydrogen bonds : angle 6.08835 ( 585) link_BETA1-4 : bond 0.00666 ( 5) link_BETA1-4 : angle 1.62344 ( 15) link_NAG-ASN : bond 0.00731 ( 11) link_NAG-ASN : angle 3.64428 ( 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 120 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 LEU cc_start: 0.4465 (mm) cc_final: 0.4233 (mt) REVERT: D 182 MET cc_start: 0.6485 (mmm) cc_final: 0.6149 (mmp) REVERT: C 131 LEU cc_start: 0.5864 (mp) cc_final: 0.5633 (tt) REVERT: B 438 SER cc_start: 0.7375 (p) cc_final: 0.7132 (m) REVERT: A 438 MET cc_start: 0.5586 (ptp) cc_final: 0.5283 (mpp) outliers start: 14 outliers final: 8 residues processed: 118 average time/residue: 0.1147 time to fit residues: 18.1719 Evaluate side-chains 91 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 268 THR 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: 6.9990 chunk 44 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS B 420 GLN B 434 HIS B 527 GLN A 478 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.185023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.164489 restraints weight = 19122.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.163844 restraints weight = 25524.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.165715 restraints weight = 20303.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.165239 restraints weight = 14849.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.165651 restraints weight = 14658.808| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9923 Z= 0.153 Angle : 0.689 9.864 13572 Z= 0.328 Chirality : 0.049 0.703 1547 Planarity : 0.004 0.045 1685 Dihedral : 9.840 81.415 1592 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.27 % Allowed : 13.99 % Favored : 83.74 % 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: -2.32 (0.23), residues: 1157 helix: 2.55 (0.47), residues: 135 sheet: -1.40 (0.26), residues: 368 loop : -2.64 (0.21), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 176 TYR 0.016 0.002 TYR D 49 PHE 0.016 0.002 PHE A 169 TRP 0.027 0.002 TRP B 246 HIS 0.027 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9899) covalent geometry : angle 0.66879 (13508) SS BOND : bond 0.00458 ( 8) SS BOND : angle 1.83839 ( 16) hydrogen bonds : bond 0.05138 ( 211) hydrogen bonds : angle 5.48588 ( 585) link_BETA1-4 : bond 0.00393 ( 5) link_BETA1-4 : angle 1.62668 ( 15) link_NAG-ASN : bond 0.00389 ( 11) link_NAG-ASN : angle 3.06003 ( 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 128 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 182 MET cc_start: 0.7158 (mmm) cc_final: 0.6893 (mmp) REVERT: C 142 ASN cc_start: 0.4889 (OUTLIER) cc_final: 0.4267 (m-40) REVERT: C 275 GLU cc_start: 0.5477 (mm-30) cc_final: 0.5187 (tm-30) REVERT: B 438 SER cc_start: 0.7333 (p) cc_final: 0.7008 (m) REVERT: A 351 TRP cc_start: 0.5834 (p90) cc_final: 0.5467 (p90) REVERT: A 438 MET cc_start: 0.5459 (ptp) cc_final: 0.5177 (mpp) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 0.1059 time to fit residues: 17.8706 Evaluate side-chains 108 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 ASN 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 222 LEU 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: 4.9990 chunk 5 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4442 r_free = 0.4442 target = 0.177134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.154847 restraints weight = 19164.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.154079 restraints weight = 24414.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.155259 restraints weight = 19931.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.155396 restraints weight = 15104.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.155562 restraints weight = 13992.986| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9923 Z= 0.178 Angle : 0.725 10.361 13572 Z= 0.347 Chirality : 0.048 0.554 1547 Planarity : 0.005 0.061 1685 Dihedral : 8.319 67.210 1592 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 3.78 % Allowed : 15.31 % Favored : 80.91 % 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: -2.25 (0.24), residues: 1157 helix: 2.55 (0.48), residues: 135 sheet: -1.43 (0.26), residues: 363 loop : -2.52 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 220 TYR 0.020 0.002 TYR C 126 PHE 0.021 0.002 PHE A 169 TRP 0.025 0.002 TRP B 246 HIS 0.019 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9899) covalent geometry : angle 0.70382 (13508) SS BOND : bond 0.00605 ( 8) SS BOND : angle 2.07437 ( 16) hydrogen bonds : bond 0.06199 ( 211) hydrogen bonds : angle 5.37101 ( 585) link_BETA1-4 : bond 0.00498 ( 5) link_BETA1-4 : angle 1.73937 ( 15) link_NAG-ASN : bond 0.00464 ( 11) link_NAG-ASN : angle 3.14650 ( 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 150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8693 (tp) REVERT: C 252 ASP cc_start: 0.5869 (OUTLIER) cc_final: 0.5637 (t0) REVERT: A 351 TRP cc_start: 0.6645 (p90) cc_final: 0.6372 (p90) outliers start: 40 outliers final: 22 residues processed: 140 average time/residue: 0.0968 time to fit residues: 19.1294 Evaluate side-chains 124 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 106 ASN 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 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 232 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 167 HIS 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: 6.9990 chunk 6 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 5 optimal weight: 0.0770 chunk 2 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 180 GLN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS B 527 GLN A 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.178929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.157958 restraints weight = 18998.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.157317 restraints weight = 23948.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.158594 restraints weight = 21059.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.158598 restraints weight = 15266.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.159056 restraints weight = 15627.385| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9923 Z= 0.124 Angle : 0.671 9.538 13572 Z= 0.317 Chirality : 0.046 0.381 1547 Planarity : 0.004 0.040 1685 Dihedral : 7.903 61.172 1592 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 2.84 % Allowed : 16.92 % Favored : 80.25 % 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: -1.99 (0.24), residues: 1157 helix: 3.13 (0.47), residues: 129 sheet: -1.23 (0.27), residues: 363 loop : -2.41 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.011 0.001 TYR D 49 PHE 0.020 0.001 PHE A 332 TRP 0.011 0.001 TRP B 246 HIS 0.004 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9899) covalent geometry : angle 0.65144 (13508) SS BOND : bond 0.00650 ( 8) SS BOND : angle 2.11979 ( 16) hydrogen bonds : bond 0.05314 ( 211) hydrogen bonds : angle 5.02669 ( 585) link_BETA1-4 : bond 0.00530 ( 5) link_BETA1-4 : angle 1.80739 ( 15) link_NAG-ASN : bond 0.00459 ( 11) link_NAG-ASN : angle 2.83979 ( 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 138 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8627 (tp) REVERT: C 245 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6938 (ptm160) REVERT: A 328 LYS cc_start: 0.6944 (tmtt) cc_final: 0.6387 (tttm) outliers start: 30 outliers final: 20 residues processed: 129 average time/residue: 0.0986 time to fit residues: 17.7920 Evaluate side-chains 122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 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 261 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 GLN B 527 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.177840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.156425 restraints weight = 19074.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.155669 restraints weight = 24448.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.156641 restraints weight = 19975.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.156832 restraints weight = 14961.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.157003 restraints weight = 14167.115| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9923 Z= 0.131 Angle : 0.674 11.285 13572 Z= 0.322 Chirality : 0.045 0.350 1547 Planarity : 0.004 0.042 1685 Dihedral : 7.505 53.235 1592 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 3.31 % Allowed : 17.20 % Favored : 79.49 % 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: -1.89 (0.24), residues: 1157 helix: 3.02 (0.47), residues: 129 sheet: -1.15 (0.27), residues: 362 loop : -2.30 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 176 TYR 0.024 0.001 TYR B 502 PHE 0.020 0.001 PHE A 332 TRP 0.020 0.001 TRP A 351 HIS 0.003 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9899) covalent geometry : angle 0.65719 (13508) SS BOND : bond 0.00709 ( 8) SS BOND : angle 2.12162 ( 16) hydrogen bonds : bond 0.05340 ( 211) hydrogen bonds : angle 4.92987 ( 585) link_BETA1-4 : bond 0.00528 ( 5) link_BETA1-4 : angle 1.81361 ( 15) link_NAG-ASN : bond 0.00444 ( 11) link_NAG-ASN : angle 2.49433 ( 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 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8656 (tp) REVERT: C 245 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7041 (ptm160) REVERT: B 393 TYR cc_start: 0.5340 (OUTLIER) cc_final: 0.5037 (p90) REVERT: A 206 LYS cc_start: 0.4053 (pptt) cc_final: 0.3259 (pptt) REVERT: A 328 LYS cc_start: 0.6945 (tmtt) cc_final: 0.6637 (tttm) REVERT: A 332 PHE cc_start: 0.5429 (OUTLIER) cc_final: 0.4798 (t80) REVERT: A 351 TRP cc_start: 0.6724 (p90) cc_final: 0.6522 (p90) outliers start: 35 outliers final: 26 residues processed: 134 average time/residue: 0.0954 time to fit residues: 17.7322 Evaluate side-chains 132 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 261 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 393 TYR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 17 optimal weight: 0.0040 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 527 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.178954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.158025 restraints weight = 19015.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.157325 restraints weight = 26313.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.158898 restraints weight = 22405.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.158641 restraints weight = 15353.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.158670 restraints weight = 14270.500| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9923 Z= 0.118 Angle : 0.666 12.621 13572 Z= 0.317 Chirality : 0.044 0.283 1547 Planarity : 0.004 0.040 1685 Dihedral : 7.054 54.465 1592 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.21 % Allowed : 17.67 % Favored : 79.11 % 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: -1.71 (0.24), residues: 1157 helix: 3.12 (0.46), residues: 129 sheet: -1.01 (0.26), residues: 365 loop : -2.18 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 176 TYR 0.009 0.001 TYR D 49 PHE 0.020 0.001 PHE A 332 TRP 0.011 0.001 TRP B 519 HIS 0.003 0.000 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9899) covalent geometry : angle 0.65046 (13508) SS BOND : bond 0.00705 ( 8) SS BOND : angle 1.81438 ( 16) hydrogen bonds : bond 0.04847 ( 211) hydrogen bonds : angle 4.67900 ( 585) link_BETA1-4 : bond 0.00535 ( 5) link_BETA1-4 : angle 1.87387 ( 15) link_NAG-ASN : bond 0.00465 ( 11) link_NAG-ASN : angle 2.43128 ( 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 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8601 (tp) REVERT: D 86 ARG cc_start: 0.6728 (mmt90) cc_final: 0.6472 (mmm160) REVERT: C 245 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7007 (ptm160) REVERT: B 393 TYR cc_start: 0.5284 (OUTLIER) cc_final: 0.4999 (p90) REVERT: A 206 LYS cc_start: 0.4133 (pptt) cc_final: 0.3330 (pptt) REVERT: A 328 LYS cc_start: 0.6917 (tmtt) cc_final: 0.6630 (tttm) REVERT: A 332 PHE cc_start: 0.5412 (OUTLIER) cc_final: 0.4818 (t80) outliers start: 34 outliers final: 22 residues processed: 136 average time/residue: 0.0958 time to fit residues: 18.4165 Evaluate side-chains 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 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 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 434 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 0.6980 chunk 79 optimal weight: 0.0570 chunk 51 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 298 HIS B 527 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.178925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.157501 restraints weight = 18922.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.156690 restraints weight = 24878.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.158042 restraints weight = 21339.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.158220 restraints weight = 16188.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.158787 restraints weight = 15389.610| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9923 Z= 0.117 Angle : 0.672 11.930 13572 Z= 0.321 Chirality : 0.044 0.271 1547 Planarity : 0.004 0.045 1685 Dihedral : 6.739 53.345 1592 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.74 % Allowed : 18.53 % Favored : 78.73 % 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: -1.67 (0.24), residues: 1157 helix: 3.15 (0.46), residues: 129 sheet: -1.05 (0.27), residues: 357 loop : -2.10 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 176 TYR 0.008 0.001 TYR D 49 PHE 0.020 0.001 PHE A 332 TRP 0.012 0.001 TRP A 351 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9899) covalent geometry : angle 0.65714 (13508) SS BOND : bond 0.00724 ( 8) SS BOND : angle 1.63974 ( 16) hydrogen bonds : bond 0.04802 ( 211) hydrogen bonds : angle 4.61959 ( 585) link_BETA1-4 : bond 0.00520 ( 5) link_BETA1-4 : angle 1.89073 ( 15) link_NAG-ASN : bond 0.00489 ( 11) link_NAG-ASN : angle 2.43323 ( 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 133 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8784 (tp) cc_final: 0.8569 (tp) REVERT: D 88 THR cc_start: 0.6942 (p) cc_final: 0.6698 (p) REVERT: C 245 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7000 (ptm160) REVERT: C 276 TYR cc_start: 0.5642 (m-10) cc_final: 0.5068 (m-10) REVERT: B 393 TYR cc_start: 0.5285 (OUTLIER) cc_final: 0.4943 (p90) REVERT: A 206 LYS cc_start: 0.4199 (pptt) cc_final: 0.3398 (pptt) REVERT: A 328 LYS cc_start: 0.6876 (tmtt) cc_final: 0.6652 (tttm) REVERT: A 332 PHE cc_start: 0.5380 (OUTLIER) cc_final: 0.4863 (t80) outliers start: 29 outliers final: 23 residues processed: 123 average time/residue: 0.0992 time to fit residues: 17.0562 Evaluate side-chains 125 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 434 HIS 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 183 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: 2.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 84 optimal weight: 0.0670 chunk 42 optimal weight: 5.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN ** B 527 GLN ** 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 = 0.4392 r_free = 0.4392 target = 0.172733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.149752 restraints weight = 19147.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.148719 restraints weight = 26512.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.149982 restraints weight = 22228.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.149979 restraints weight = 15453.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.150146 restraints weight = 14926.528| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9923 Z= 0.164 Angle : 0.730 11.421 13572 Z= 0.354 Chirality : 0.046 0.250 1547 Planarity : 0.005 0.056 1685 Dihedral : 6.753 54.119 1592 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 3.12 % Allowed : 18.43 % Favored : 78.45 % 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: -1.84 (0.24), residues: 1157 helix: 3.01 (0.46), residues: 126 sheet: -1.17 (0.26), residues: 364 loop : -2.19 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 176 TYR 0.012 0.002 TYR D 49 PHE 0.019 0.002 PHE A 332 TRP 0.016 0.002 TRP C 232 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9899) covalent geometry : angle 0.71557 (13508) SS BOND : bond 0.00715 ( 8) SS BOND : angle 1.77357 ( 16) hydrogen bonds : bond 0.06166 ( 211) hydrogen bonds : angle 4.85559 ( 585) link_BETA1-4 : bond 0.00458 ( 5) link_BETA1-4 : angle 1.89469 ( 15) link_NAG-ASN : bond 0.00471 ( 11) link_NAG-ASN : angle 2.49969 ( 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 140 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8737 (tp) REVERT: C 236 GLU cc_start: 0.6197 (mm-30) cc_final: 0.5930 (mm-30) REVERT: C 245 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7314 (ptm160) REVERT: B 393 TYR cc_start: 0.5392 (OUTLIER) cc_final: 0.5102 (p90) REVERT: A 206 LYS cc_start: 0.4565 (pptt) cc_final: 0.3649 (pptt) REVERT: A 305 ASP cc_start: 0.7755 (p0) cc_final: 0.7554 (p0) REVERT: A 328 LYS cc_start: 0.6910 (tmtt) cc_final: 0.6587 (tttm) REVERT: A 332 PHE cc_start: 0.5773 (OUTLIER) cc_final: 0.4859 (t80) outliers start: 33 outliers final: 26 residues processed: 127 average time/residue: 0.1023 time to fit residues: 18.0492 Evaluate side-chains 131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 151 MET 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 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 434 HIS 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 105 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 93 optimal weight: 0.0050 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.175076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.152593 restraints weight = 18980.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.151825 restraints weight = 23934.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.153046 restraints weight = 19967.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.153029 restraints weight = 14634.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.153213 restraints weight = 13867.493| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9923 Z= 0.126 Angle : 0.681 10.823 13572 Z= 0.330 Chirality : 0.044 0.241 1547 Planarity : 0.004 0.055 1685 Dihedral : 6.513 54.328 1592 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.65 % Allowed : 18.81 % Favored : 78.54 % 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: -1.72 (0.24), residues: 1157 helix: 3.20 (0.45), residues: 126 sheet: -1.09 (0.27), residues: 364 loop : -2.14 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 176 TYR 0.011 0.001 TYR D 49 PHE 0.015 0.001 PHE A 332 TRP 0.011 0.001 TRP A 351 HIS 0.005 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9899) covalent geometry : angle 0.66710 (13508) SS BOND : bond 0.00677 ( 8) SS BOND : angle 1.55816 ( 16) hydrogen bonds : bond 0.05400 ( 211) hydrogen bonds : angle 4.69496 ( 585) link_BETA1-4 : bond 0.00478 ( 5) link_BETA1-4 : angle 1.83846 ( 15) link_NAG-ASN : bond 0.00523 ( 11) link_NAG-ASN : angle 2.44125 ( 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 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8681 (tp) REVERT: D 154 LEU cc_start: 0.8610 (mm) cc_final: 0.8338 (mp) REVERT: C 236 GLU cc_start: 0.6190 (mm-30) cc_final: 0.5926 (mm-30) REVERT: C 245 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7025 (ptm160) REVERT: C 275 GLU cc_start: 0.5712 (mm-30) cc_final: 0.5029 (tm-30) REVERT: B 275 GLU cc_start: 0.7712 (mp0) cc_final: 0.7349 (mp0) REVERT: B 393 TYR cc_start: 0.5405 (OUTLIER) cc_final: 0.5071 (p90) REVERT: A 206 LYS cc_start: 0.4624 (pptt) cc_final: 0.3693 (pptt) REVERT: A 328 LYS cc_start: 0.6653 (tmtt) cc_final: 0.6401 (tttm) REVERT: A 332 PHE cc_start: 0.5684 (OUTLIER) cc_final: 0.4795 (t80) REVERT: A 348 GLN cc_start: 0.7108 (tp-100) cc_final: 0.6891 (tt0) outliers start: 28 outliers final: 21 residues processed: 118 average time/residue: 0.0932 time to fit residues: 15.7693 Evaluate side-chains 123 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 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 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 434 HIS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.173089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.152037 restraints weight = 18971.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.151237 restraints weight = 26796.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.152432 restraints weight = 23038.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.152218 restraints weight = 15862.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.152298 restraints weight = 16530.954| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9923 Z= 0.140 Angle : 0.692 10.195 13572 Z= 0.336 Chirality : 0.045 0.232 1547 Planarity : 0.005 0.056 1685 Dihedral : 6.466 54.939 1592 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.65 % Allowed : 19.09 % Favored : 78.26 % 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: -1.76 (0.24), residues: 1157 helix: 3.19 (0.46), residues: 126 sheet: -1.18 (0.27), residues: 364 loop : -2.12 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 176 TYR 0.020 0.001 TYR B 502 PHE 0.020 0.001 PHE A 332 TRP 0.013 0.001 TRP C 232 HIS 0.004 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9899) covalent geometry : angle 0.67875 (13508) SS BOND : bond 0.00669 ( 8) SS BOND : angle 1.56531 ( 16) hydrogen bonds : bond 0.05678 ( 211) hydrogen bonds : angle 4.71243 ( 585) link_BETA1-4 : bond 0.00427 ( 5) link_BETA1-4 : angle 1.79062 ( 15) link_NAG-ASN : bond 0.00507 ( 11) link_NAG-ASN : angle 2.42834 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.83 seconds wall clock time: 28 minutes 28.25 seconds (1708.25 seconds total)