Starting phenix.real_space_refine on Sat Jul 4 09:36:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t5w_55597/07_2026/9t5w_55597_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t5w_55597/07_2026/9t5w_55597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t5w_55597/07_2026/9t5w_55597_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t5w_55597/07_2026/9t5w_55597_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t5w_55597/07_2026/9t5w_55597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t5w_55597/07_2026/9t5w_55597.map" } resolution = 2.74 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= 0.027 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 Mn 1 7.51 5 S 54 5.16 5 C 6007 2.51 5 N 1682 2.21 5 O 1898 1.98 5 H 9204 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18851 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 11519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 11519 Classifications: {'peptide': 751} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 715} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 7060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7060 Classifications: {'peptide': 459} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 434} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' MN': 1, ' CA': 2} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.42, per 1000 atoms: 0.18 Number of scatterers: 18851 At special positions: 0 Unit cell: (68.37, 152.22, 187.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 1 24.99 Ca 5 19.99 S 54 16.00 O 1898 8.00 N 1682 7.00 C 6007 6.00 H 9204 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS A 706 " distance=2.03 Simple disulfide: pdb=" SG CYS A 639 " - pdb=" SG CYS A 696 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 21 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 450 " - pdb=" SG CYS B 459 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1204 " - " ASN A 677 " " NAG A1205 " - " ASN A 681 " " NAG B2004 " - " ASN B 232 " " NAG C 1 " - " ASN A 719 " " NAG D 1 " - " ASN A 70 " " NAG E 1 " - " ASN A 375 " " NAG F 1 " - " ASN B 190 " " NAG G 1 " - " ASN B 94 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 653.3 milliseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2216 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 19.5% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 194 through 200 removed outlier: 4.054A pdb=" N LEU A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 255 through 262 removed outlier: 3.605A pdb=" N GLU A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 558 through 562 Processing helix chain 'B' and resid 10 through 18 removed outlier: 4.021A pdb=" N GLY B 18 " --> pdb=" O CYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.568A pdb=" N ILE B 38 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.346A pdb=" N MET B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 120 through 139 removed outlier: 3.516A pdb=" N GLY B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.540A pdb=" N GLN B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 273 through 277 removed outlier: 3.755A pdb=" N PHE B 277 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 304 through 315 removed outlier: 3.745A pdb=" N GLU B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 341 removed outlier: 3.626A pdb=" N VAL B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.948A pdb=" N GLY B 439 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.723A pdb=" N MET A 9 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP A 585 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A 575 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 80 removed outlier: 4.135A pdb=" N THR A 92 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS A 104 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS A 94 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N TYR A 102 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 184 removed outlier: 6.666A pdb=" N LEU A 173 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 236 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 238 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 138 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 140 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS A 235 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N TYR A 267 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 237 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE A 269 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 239 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 396 removed outlier: 3.731A pdb=" N ALA A 391 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLN A 401 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN A 421 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 430 " --> pdb=" O MET A 418 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG A 420 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER A 428 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASN A 422 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.470A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 492 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 509 through 513 removed outlier: 6.177A pdb=" N ASP A 522 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.768A pdb=" N GLY A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 675 through 676 removed outlier: 3.913A pdb=" N GLY A 634 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 690 Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AB4, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.601A pdb=" N THR B 394 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N SER B 362 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG B 371 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 80 through 82 removed outlier: 7.021A pdb=" N VAL B 81 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 343 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 345 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ASP B 379 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 347 " --> pdb=" O ASP B 377 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP B 377 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 186 through 189 removed outlier: 4.678A pdb=" N LEU B 188 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 105 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLY B 145 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 107 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG B 235 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE B 297 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 237 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA B 299 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE B 239 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 319 " --> pdb=" O PRO B 296 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9203 1.03 - 1.23: 224 1.23 - 1.43: 3891 1.43 - 1.63: 5628 1.63 - 1.83: 73 Bond restraints: 19019 Sorted by residual: bond pdb=" N ILE B 455 " pdb=" CA ILE B 455 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.19e-02 7.06e+03 9.72e+00 bond pdb=" N LYS B 457 " pdb=" CA LYS B 457 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.23e-02 6.61e+03 7.58e+00 bond pdb=" N TYR B 454 " pdb=" CA TYR B 454 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.97e+00 bond pdb=" N ARG A 487 " pdb=" CA ARG A 487 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.82e+00 bond pdb=" N LEU A 480 " pdb=" CA LEU A 480 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.29e-02 6.01e+03 5.81e+00 ... (remaining 19014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 33162 2.02 - 4.04: 932 4.04 - 6.06: 104 6.06 - 8.08: 21 8.08 - 10.10: 5 Bond angle restraints: 34224 Sorted by residual: angle pdb=" CA TYR B 84 " pdb=" CB TYR B 84 " pdb=" CG TYR B 84 " ideal model delta sigma weight residual 113.90 121.24 -7.34 1.80e+00 3.09e-01 1.66e+01 angle pdb=" CA ASN B 458 " pdb=" C ASN B 458 " pdb=" O ASN B 458 " ideal model delta sigma weight residual 122.27 117.88 4.39 1.16e+00 7.43e-01 1.43e+01 angle pdb=" C PRO B 170 " pdb=" N ASN B 171 " pdb=" CA ASN B 171 " ideal model delta sigma weight residual 121.54 128.58 -7.04 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N GLY B 453 " pdb=" CA GLY B 453 " pdb=" C GLY B 453 " ideal model delta sigma weight residual 114.66 110.11 4.55 1.24e+00 6.50e-01 1.35e+01 angle pdb=" CA ARG A 126 " pdb=" C ARG A 126 " pdb=" O ARG A 126 " ideal model delta sigma weight residual 121.44 117.52 3.92 1.08e+00 8.57e-01 1.32e+01 ... (remaining 34219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.05: 8392 23.05 - 46.10: 673 46.10 - 69.15: 172 69.15 - 92.20: 20 92.20 - 115.24: 34 Dihedral angle restraints: 9291 sinusoidal: 5319 harmonic: 3972 Sorted by residual: dihedral pdb=" CD ARG A 482 " pdb=" NE ARG A 482 " pdb=" CZ ARG A 482 " pdb=" NH1 ARG A 482 " ideal model delta sinusoidal sigma weight residual 0.00 70.74 -70.74 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CD ARG A 485 " pdb=" NE ARG A 485 " pdb=" CZ ARG A 485 " pdb=" NH1 ARG A 485 " ideal model delta sinusoidal sigma weight residual 0.00 -62.98 62.98 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CA SER A 82 " pdb=" C SER A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual -180.00 -146.99 -33.01 0 5.00e+00 4.00e-02 4.36e+01 ... (remaining 9288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1347 0.077 - 0.154: 177 0.154 - 0.232: 9 0.232 - 0.309: 1 0.309 - 0.386: 1 Chirality restraints: 1535 Sorted by residual: chirality pdb=" C1 NAG A1204 " pdb=" ND2 ASN A 677 " pdb=" C2 NAG A1204 " pdb=" O5 NAG A1204 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 719 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1 NAG A1205 " pdb=" ND2 ASN A 681 " pdb=" C2 NAG A1205 " pdb=" O5 NAG A1205 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1532 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 487 " 0.563 9.50e-02 1.11e+02 2.23e-01 3.63e+02 pdb=" NE ARG A 487 " 0.083 2.00e-02 2.50e+03 pdb=" CZ ARG A 487 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 487 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 487 " -0.030 2.00e-02 2.50e+03 pdb="HH11 ARG A 487 " -0.248 2.00e-02 2.50e+03 pdb="HH12 ARG A 487 " 0.236 2.00e-02 2.50e+03 pdb="HH21 ARG A 487 " -0.027 2.00e-02 2.50e+03 pdb="HH22 ARG A 487 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 485 " 0.946 9.50e-02 1.11e+02 3.27e-01 2.73e+02 pdb=" NE ARG A 485 " -0.094 2.00e-02 2.50e+03 pdb=" CZ ARG A 485 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG A 485 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 485 " 0.023 2.00e-02 2.50e+03 pdb="HH11 ARG A 485 " 0.145 2.00e-02 2.50e+03 pdb="HH12 ARG A 485 " -0.156 2.00e-02 2.50e+03 pdb="HH21 ARG A 485 " -0.027 2.00e-02 2.50e+03 pdb="HH22 ARG A 485 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 482 " 1.096 9.50e-02 1.11e+02 3.66e-01 1.50e+02 pdb=" NE ARG A 482 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 482 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 482 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 482 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG A 482 " -0.042 2.00e-02 2.50e+03 pdb="HH12 ARG A 482 " 0.055 2.00e-02 2.50e+03 pdb="HH21 ARG A 482 " 0.012 2.00e-02 2.50e+03 pdb="HH22 ARG A 482 " -0.013 2.00e-02 2.50e+03 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 6193 2.36 - 2.92: 42340 2.92 - 3.48: 48721 3.48 - 4.04: 66902 4.04 - 4.60: 98309 Nonbonded interactions: 262465 Sorted by model distance: nonbonded pdb="HD11 ILE A 319 " pdb=" HD3 PRO B 170 " model vdw 1.797 2.440 nonbonded pdb=" H ASN B 207 " pdb="HD21 ASN B 207 " model vdw 1.811 2.100 nonbonded pdb=" HG3 GLU A 131 " pdb=" HA LYS A 315 " model vdw 1.827 2.440 nonbonded pdb=" OE1 GLU A 314 " pdb=" H GLU A 314 " model vdw 1.911 2.450 nonbonded pdb=" H SER A 340 " pdb=" HG SER A 351 " model vdw 1.935 2.100 ... (remaining 262460 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 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.110 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 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 : 0.005 0.084 9852 Z= 0.237 Angle : 0.935 14.368 13381 Z= 0.475 Chirality : 0.052 0.386 1535 Planarity : 0.018 0.471 1735 Dihedral : 19.078 115.244 3970 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.22 % Favored : 93.62 % Rotamer: Outliers : 0.87 % Allowed : 20.60 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.09 % 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: -2.23 (0.23), residues: 1206 helix: -0.28 (0.37), residues: 182 sheet: -1.49 (0.26), residues: 366 loop : -1.81 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 115 TYR 0.015 0.001 TYR B 84 PHE 0.020 0.002 PHE B 404 TRP 0.007 0.002 TRP B 230 HIS 0.006 0.001 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 ( 9815) covalent geometry : angle 0.91220 / 0.47 (13287) SS BOND : bond 0.00272 / 0.11 ( 17) SS BOND : angle 1.11696 / 0.67 ( 34) hydrogen bonds : bond 0.15739 / 10.93 ( 306) hydrogen bonds : angle 7.48410 / 5.17 ( 810) link_ALPHA1-3 : bond 0.01083 / 0.52 ( 2) link_ALPHA1-3 : angle 2.37723 / 1.76 ( 6) link_ALPHA1-6 : bond 0.00512 / 0.24 ( 2) link_ALPHA1-6 : angle 1.57375 / 1.33 ( 6) link_BETA1-4 : bond 0.00461 / 0.22 ( 8) link_BETA1-4 : angle 2.54205 / 2.17 ( 24) link_NAG-ASN : bond 0.01079 / 0.63 ( 8) link_NAG-ASN : angle 3.99697 / 2.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.7279 (mm) cc_final: 0.7055 (mm) REVERT: A 580 MET cc_start: 0.7540 (mtm) cc_final: 0.7331 (mtp) REVERT: A 585 ASP cc_start: 0.5890 (m-30) cc_final: 0.5066 (m-30) REVERT: A 602 VAL cc_start: 0.8557 (m) cc_final: 0.8161 (t) REVERT: B 57 MET cc_start: 0.5762 (tpp) cc_final: 0.5312 (tpp) REVERT: B 394 THR cc_start: 0.6365 (m) cc_final: 0.5996 (m) outliers start: 9 outliers final: 2 residues processed: 180 average time/residue: 0.7933 time to fit residues: 159.8962 Evaluate side-chains 107 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 ASN Chi-restraints excluded: chain B residue 94 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 HIS A 600 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.137738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088274 restraints weight = 49188.114| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.01 r_work: 0.3251 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 9852 Z= 0.203 Angle : 0.746 9.512 13381 Z= 0.368 Chirality : 0.050 0.322 1535 Planarity : 0.006 0.136 1735 Dihedral : 10.764 113.315 1720 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 3.68 % Allowed : 22.34 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -2.01 (0.23), residues: 1206 helix: 0.58 (0.37), residues: 184 sheet: -1.61 (0.25), residues: 375 loop : -1.73 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 482 TYR 0.015 0.002 TYR A 661 PHE 0.019 0.002 PHE A 749 TRP 0.022 0.003 TRP B 23 HIS 0.016 0.002 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 9815) covalent geometry : angle 0.72340 / 0.36 (13287) SS BOND : bond 0.00233 / 0.12 ( 17) SS BOND : angle 0.78619 / 0.48 ( 34) hydrogen bonds : bond 0.03691 / 2.36 ( 306) hydrogen bonds : angle 6.15313 / 4.24 ( 810) link_ALPHA1-3 : bond 0.00347 / 0.17 ( 2) link_ALPHA1-3 : angle 3.09043 / 2.00 ( 6) link_ALPHA1-6 : bond 0.00620 / 0.30 ( 2) link_ALPHA1-6 : angle 3.15100 / 2.94 ( 6) link_BETA1-4 : bond 0.00489 / 0.28 ( 8) link_BETA1-4 : angle 1.98992 / 1.37 ( 24) link_NAG-ASN : bond 0.00530 / 0.27 ( 8) link_NAG-ASN : angle 3.25248 / 2.40 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.7858 (tmm) cc_final: 0.7563 (ppp) REVERT: A 398 ASN cc_start: 0.7965 (t0) cc_final: 0.7621 (p0) REVERT: A 451 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7106 (p0) REVERT: A 660 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8552 (p) REVERT: B 57 MET cc_start: 0.5915 (tpp) cc_final: 0.5704 (tpp) REVERT: B 309 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7371 (mm-30) outliers start: 38 outliers final: 10 residues processed: 106 average time/residue: 0.7120 time to fit residues: 86.1674 Evaluate side-chains 76 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 309 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 HIS A 332 HIS A 401 GLN A 600 GLN A 702 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.137161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087256 restraints weight = 49292.095| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.07 r_work: 0.3226 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9852 Z= 0.163 Angle : 0.712 16.750 13381 Z= 0.337 Chirality : 0.049 0.312 1535 Planarity : 0.005 0.133 1735 Dihedral : 8.339 111.191 1718 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 2.80 % Allowed : 22.24 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1206 helix: 0.87 (0.38), residues: 185 sheet: -1.61 (0.25), residues: 378 loop : -1.47 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 487 TYR 0.019 0.002 TYR B 109 PHE 0.021 0.002 PHE A 749 TRP 0.009 0.001 TRP A 358 HIS 0.004 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 9815) covalent geometry : angle 0.69272 / 0.33 (13287) SS BOND : bond 0.00292 / 0.12 ( 17) SS BOND : angle 0.79913 / 0.45 ( 34) hydrogen bonds : bond 0.03990 / 2.60 ( 306) hydrogen bonds : angle 5.79103 / 4.00 ( 810) link_ALPHA1-3 : bond 0.01218 / 0.58 ( 2) link_ALPHA1-3 : angle 2.12858 / 1.50 ( 6) link_ALPHA1-6 : bond 0.00835 / 0.40 ( 2) link_ALPHA1-6 : angle 2.13196 / 1.30 ( 6) link_BETA1-4 : bond 0.00441 / 0.26 ( 8) link_BETA1-4 : angle 1.94195 / 1.65 ( 24) link_NAG-ASN : bond 0.00707 / 0.39 ( 8) link_NAG-ASN : angle 3.21785 / 2.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8178 (tmm) cc_final: 0.7752 (ttm) REVERT: A 81 THR cc_start: 0.8304 (m) cc_final: 0.8044 (p) REVERT: A 610 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.5935 (tm-30) REVERT: A 660 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8564 (p) REVERT: A 702 GLN cc_start: 0.6938 (mt0) cc_final: 0.6614 (mm-40) REVERT: B 57 MET cc_start: 0.5846 (OUTLIER) cc_final: 0.5617 (tpp) REVERT: B 266 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8280 (mp) REVERT: B 309 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: B 394 THR cc_start: 0.7087 (m) cc_final: 0.6771 (m) outliers start: 29 outliers final: 7 residues processed: 79 average time/residue: 0.6697 time to fit residues: 60.9652 Evaluate side-chains 58 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 378 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS A 401 GLN A 694 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.136435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086240 restraints weight = 49195.766| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.07 r_work: 0.3202 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9852 Z= 0.162 Angle : 0.652 17.972 13381 Z= 0.314 Chirality : 0.047 0.256 1535 Planarity : 0.006 0.175 1735 Dihedral : 8.170 112.622 1718 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 2.61 % Allowed : 21.47 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -1.64 (0.24), residues: 1206 helix: 1.23 (0.39), residues: 185 sheet: -1.57 (0.25), residues: 377 loop : -1.46 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.013 0.001 TYR A 661 PHE 0.010 0.001 PHE A 121 TRP 0.008 0.001 TRP A 358 HIS 0.003 0.001 HIS A 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9815) covalent geometry : angle 0.62746 / 0.31 (13287) SS BOND : bond 0.00212 / 0.09 ( 17) SS BOND : angle 1.74645 / 0.82 ( 34) hydrogen bonds : bond 0.03164 / 2.04 ( 306) hydrogen bonds : angle 5.68668 / 3.94 ( 810) link_ALPHA1-3 : bond 0.00856 / 0.41 ( 2) link_ALPHA1-3 : angle 2.75141 / 1.78 ( 6) link_ALPHA1-6 : bond 0.00928 / 0.44 ( 2) link_ALPHA1-6 : angle 1.59689 / 1.29 ( 6) link_BETA1-4 : bond 0.00286 / 0.18 ( 8) link_BETA1-4 : angle 1.98876 / 1.62 ( 24) link_NAG-ASN : bond 0.00529 / 0.30 ( 8) link_NAG-ASN : angle 2.92248 / 2.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.5861 (tm-30) REVERT: A 660 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8687 (p) REVERT: A 702 GLN cc_start: 0.6786 (mt0) cc_final: 0.6499 (mm-40) REVERT: B 394 THR cc_start: 0.7351 (m) cc_final: 0.7058 (m) outliers start: 27 outliers final: 12 residues processed: 69 average time/residue: 0.8206 time to fit residues: 63.7230 Evaluate side-chains 54 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 378 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS A 401 GLN A 694 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.134234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083037 restraints weight = 49167.164| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.03 r_work: 0.3144 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.6262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 9852 Z= 0.208 Angle : 0.698 18.558 13381 Z= 0.336 Chirality : 0.048 0.289 1535 Planarity : 0.006 0.173 1735 Dihedral : 7.654 110.477 1718 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer: Outliers : 2.90 % Allowed : 21.57 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -1.58 (0.24), residues: 1206 helix: 1.16 (0.39), residues: 185 sheet: -1.57 (0.25), residues: 381 loop : -1.34 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.010 0.002 TYR A 661 PHE 0.016 0.001 PHE A 121 TRP 0.007 0.002 TRP B 230 HIS 0.005 0.001 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 ( 9815) covalent geometry : angle 0.66768 / 0.33 (13287) SS BOND : bond 0.00457 / 0.20 ( 17) SS BOND : angle 2.40177 / 1.01 ( 34) hydrogen bonds : bond 0.03419 / 2.19 ( 306) hydrogen bonds : angle 5.69355 / 3.95 ( 810) link_ALPHA1-3 : bond 0.01326 / 0.63 ( 2) link_ALPHA1-3 : angle 2.93521 / 1.89 ( 6) link_ALPHA1-6 : bond 0.00588 / 0.28 ( 2) link_ALPHA1-6 : angle 1.84231 / 1.57 ( 6) link_BETA1-4 : bond 0.00382 / 0.25 ( 8) link_BETA1-4 : angle 2.12446 / 1.79 ( 24) link_NAG-ASN : bond 0.01291 / 0.65 ( 8) link_NAG-ASN : angle 2.98574 / 2.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 40 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7868 (tt0) cc_final: 0.7611 (tt0) REVERT: A 402 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8262 (t) REVERT: A 610 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.5902 (tm-30) REVERT: A 651 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6998 (mtm110) REVERT: A 660 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8779 (p) REVERT: A 694 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8589 (tp40) REVERT: B 57 MET cc_start: 0.6146 (tpp) cc_final: 0.5903 (tpp) REVERT: B 117 MET cc_start: 0.8189 (mtp) cc_final: 0.7925 (mtp) REVERT: B 267 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: B 372 ASN cc_start: 0.7828 (m-40) cc_final: 0.7055 (p0) REVERT: B 394 THR cc_start: 0.7545 (m) cc_final: 0.7334 (m) outliers start: 30 outliers final: 8 residues processed: 66 average time/residue: 0.7459 time to fit residues: 55.6421 Evaluate side-chains 52 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 378 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS A 401 GLN A 694 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.134114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082944 restraints weight = 48907.463| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.02 r_work: 0.3141 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9852 Z= 0.169 Angle : 0.620 12.928 13381 Z= 0.305 Chirality : 0.046 0.216 1535 Planarity : 0.005 0.154 1735 Dihedral : 7.627 111.249 1718 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.14 % Favored : 94.69 % Rotamer: Outliers : 2.42 % Allowed : 22.63 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -1.50 (0.24), residues: 1206 helix: 1.20 (0.39), residues: 191 sheet: -1.45 (0.25), residues: 365 loop : -1.36 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 126 TYR 0.012 0.001 TYR A 661 PHE 0.016 0.001 PHE A 121 TRP 0.008 0.002 TRP B 230 HIS 0.004 0.001 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 9815) covalent geometry : angle 0.59508 / 0.30 (13287) SS BOND : bond 0.00391 / 0.17 ( 17) SS BOND : angle 1.56125 / 0.69 ( 34) hydrogen bonds : bond 0.03273 / 2.10 ( 306) hydrogen bonds : angle 5.62390 / 3.89 ( 810) link_ALPHA1-3 : bond 0.00784 / 0.37 ( 2) link_ALPHA1-3 : angle 2.59212 / 1.68 ( 6) link_ALPHA1-6 : bond 0.01006 / 0.48 ( 2) link_ALPHA1-6 : angle 1.65595 / 1.32 ( 6) link_BETA1-4 : bond 0.00301 / 0.19 ( 8) link_BETA1-4 : angle 2.10759 / 1.76 ( 24) link_NAG-ASN : bond 0.00524 / 0.30 ( 8) link_NAG-ASN : angle 2.81351 / 2.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 38 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7736 (tt0) cc_final: 0.7136 (tm-30) REVERT: A 402 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8283 (t) REVERT: A 440 TYR cc_start: 0.9268 (OUTLIER) cc_final: 0.8613 (t80) REVERT: A 610 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.5809 (tm-30) REVERT: A 651 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7361 (mtm110) REVERT: A 660 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8628 (p) REVERT: B 117 MET cc_start: 0.8225 (mtp) cc_final: 0.7975 (mtp) REVERT: B 267 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: B 394 THR cc_start: 0.7586 (m) cc_final: 0.7373 (m) outliers start: 25 outliers final: 7 residues processed: 60 average time/residue: 0.7650 time to fit residues: 51.8936 Evaluate side-chains 51 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 378 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 20 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS A 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.134208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.082800 restraints weight = 48961.147| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.05 r_work: 0.3139 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9852 Z= 0.144 Angle : 0.604 12.571 13381 Z= 0.297 Chirality : 0.046 0.259 1535 Planarity : 0.005 0.140 1735 Dihedral : 7.396 109.499 1718 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.11 % Rotamer: Outliers : 2.22 % Allowed : 22.24 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -1.39 (0.24), residues: 1206 helix: 1.30 (0.39), residues: 191 sheet: -1.39 (0.25), residues: 367 loop : -1.29 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 426 TYR 0.011 0.001 TYR A 661 PHE 0.014 0.001 PHE A 121 TRP 0.006 0.001 TRP B 230 HIS 0.003 0.001 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 9815) covalent geometry : angle 0.58046 / 0.29 (13287) SS BOND : bond 0.00296 / 0.13 ( 17) SS BOND : angle 1.59974 / 0.69 ( 34) hydrogen bonds : bond 0.03127 / 1.95 ( 306) hydrogen bonds : angle 5.51720 / 3.81 ( 810) link_ALPHA1-3 : bond 0.00968 / 0.46 ( 2) link_ALPHA1-3 : angle 2.63845 / 1.73 ( 6) link_ALPHA1-6 : bond 0.00881 / 0.42 ( 2) link_ALPHA1-6 : angle 1.58824 / 1.26 ( 6) link_BETA1-4 : bond 0.00281 / 0.17 ( 8) link_BETA1-4 : angle 2.07866 / 1.72 ( 24) link_NAG-ASN : bond 0.01075 / 0.56 ( 8) link_NAG-ASN : angle 2.61520 / 2.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7862 (tt0) cc_final: 0.7617 (tt0) REVERT: A 402 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8377 (t) REVERT: A 440 TYR cc_start: 0.9249 (OUTLIER) cc_final: 0.8522 (t80) REVERT: A 610 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.5563 (tm-30) REVERT: A 651 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7372 (mtm110) REVERT: A 660 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8470 (p) REVERT: B 57 MET cc_start: 0.6259 (tpp) cc_final: 0.5986 (tpp) outliers start: 23 outliers final: 8 residues processed: 61 average time/residue: 0.8227 time to fit residues: 56.2740 Evaluate side-chains 48 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 378 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.133819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082307 restraints weight = 48964.043| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.06 r_work: 0.3127 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9852 Z= 0.148 Angle : 0.592 11.595 13381 Z= 0.292 Chirality : 0.045 0.228 1535 Planarity : 0.005 0.136 1735 Dihedral : 7.390 109.794 1718 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 2.03 % Allowed : 21.86 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -1.29 (0.24), residues: 1206 helix: 1.36 (0.39), residues: 191 sheet: -1.33 (0.26), residues: 360 loop : -1.23 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 344 TYR 0.020 0.001 TYR A 661 PHE 0.015 0.001 PHE A 121 TRP 0.007 0.001 TRP B 230 HIS 0.003 0.001 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9815) covalent geometry : angle 0.56824 / 0.29 (13287) SS BOND : bond 0.00493 / 0.33 ( 17) SS BOND : angle 1.55649 / 0.68 ( 34) hydrogen bonds : bond 0.03070 / 1.94 ( 306) hydrogen bonds : angle 5.48005 / 3.78 ( 810) link_ALPHA1-3 : bond 0.00848 / 0.40 ( 2) link_ALPHA1-3 : angle 2.52351 / 1.66 ( 6) link_ALPHA1-6 : bond 0.00878 / 0.42 ( 2) link_ALPHA1-6 : angle 1.56433 / 1.20 ( 6) link_BETA1-4 : bond 0.00266 / 0.16 ( 8) link_BETA1-4 : angle 2.09646 / 1.72 ( 24) link_NAG-ASN : bond 0.00494 / 0.28 ( 8) link_NAG-ASN : angle 2.62714 / 2.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LEU cc_start: 0.3936 (OUTLIER) cc_final: 0.3527 (mm) REVERT: A 174 MET cc_start: 0.2461 (tmm) cc_final: 0.1603 (tmm) REVERT: A 331 GLU cc_start: 0.7767 (tt0) cc_final: 0.7205 (tm-30) REVERT: A 383 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: A 440 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8406 (t80) REVERT: A 610 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.5704 (tm-30) REVERT: A 618 ARG cc_start: 0.5501 (mpt180) cc_final: 0.5238 (mmt180) REVERT: A 660 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 57 MET cc_start: 0.6330 (tpp) cc_final: 0.6074 (tpp) REVERT: B 267 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8022 (mp0) outliers start: 21 outliers final: 7 residues processed: 56 average time/residue: 0.9154 time to fit residues: 57.0033 Evaluate side-chains 52 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 378 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 HIS A 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.133404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081911 restraints weight = 48656.754| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.07 r_work: 0.3114 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.7337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9852 Z= 0.146 Angle : 0.591 11.502 13381 Z= 0.292 Chirality : 0.045 0.235 1535 Planarity : 0.005 0.132 1735 Dihedral : 7.311 109.492 1718 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 1.55 % Allowed : 22.05 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -1.23 (0.24), residues: 1206 helix: 1.40 (0.39), residues: 191 sheet: -1.27 (0.26), residues: 359 loop : -1.19 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 618 TYR 0.010 0.001 TYR B 308 PHE 0.016 0.001 PHE A 121 TRP 0.006 0.001 TRP B 230 HIS 0.005 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9815) covalent geometry : angle 0.56671 / 0.29 (13287) SS BOND : bond 0.00313 / 0.15 ( 17) SS BOND : angle 1.63375 / 0.74 ( 34) hydrogen bonds : bond 0.03067 / 1.94 ( 306) hydrogen bonds : angle 5.46180 / 3.78 ( 810) link_ALPHA1-3 : bond 0.01064 / 0.51 ( 2) link_ALPHA1-3 : angle 2.68163 / 1.75 ( 6) link_ALPHA1-6 : bond 0.00812 / 0.39 ( 2) link_ALPHA1-6 : angle 1.51488 / 1.18 ( 6) link_BETA1-4 : bond 0.00225 / 0.13 ( 8) link_BETA1-4 : angle 2.07475 / 1.70 ( 24) link_NAG-ASN : bond 0.00692 / 0.38 ( 8) link_NAG-ASN : angle 2.58142 / 2.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7996 (tt0) cc_final: 0.7764 (tt0) REVERT: A 440 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8302 (t80) REVERT: A 660 THR cc_start: 0.8962 (p) cc_final: 0.8678 (p) REVERT: B 57 MET cc_start: 0.6256 (tpp) cc_final: 0.5989 (tpp) REVERT: B 377 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7774 (p0) outliers start: 16 outliers final: 8 residues processed: 53 average time/residue: 0.7149 time to fit residues: 42.7660 Evaluate side-chains 46 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 378 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.0770 chunk 96 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.133056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.081492 restraints weight = 48633.279| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.01 r_work: 0.3114 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9852 Z= 0.153 Angle : 0.589 11.382 13381 Z= 0.292 Chirality : 0.045 0.223 1535 Planarity : 0.005 0.130 1735 Dihedral : 7.326 109.684 1718 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 1.16 % Allowed : 22.53 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -1.21 (0.24), residues: 1206 helix: 1.43 (0.39), residues: 191 sheet: -1.25 (0.26), residues: 359 loop : -1.19 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 86 TYR 0.014 0.001 TYR A 661 PHE 0.018 0.001 PHE A 121 TRP 0.007 0.001 TRP B 230 HIS 0.004 0.001 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 9815) covalent geometry : angle 0.56512 / 0.29 (13287) SS BOND : bond 0.00309 / 0.13 ( 17) SS BOND : angle 1.57217 / 0.68 ( 34) hydrogen bonds : bond 0.03113 / 1.97 ( 306) hydrogen bonds : angle 5.44331 / 3.77 ( 810) link_ALPHA1-3 : bond 0.00919 / 0.44 ( 2) link_ALPHA1-3 : angle 2.56268 / 1.68 ( 6) link_ALPHA1-6 : bond 0.00793 / 0.38 ( 2) link_ALPHA1-6 : angle 1.51211 / 1.15 ( 6) link_BETA1-4 : bond 0.00254 / 0.15 ( 8) link_BETA1-4 : angle 2.09449 / 1.71 ( 24) link_NAG-ASN : bond 0.00544 / 0.32 ( 8) link_NAG-ASN : angle 2.55982 / 1.98 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 579 is missing expected H atoms. Skipping. Residue THR 693 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7825 (tt0) cc_final: 0.7621 (tt0) REVERT: A 440 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8255 (t80) REVERT: A 660 THR cc_start: 0.8993 (p) cc_final: 0.8696 (p) REVERT: B 57 MET cc_start: 0.6309 (tpp) cc_final: 0.6031 (tpp) REVERT: B 172 LYS cc_start: 0.8466 (mptt) cc_final: 0.8222 (mptt) REVERT: B 267 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: B 377 ASP cc_start: 0.8116 (p0) cc_final: 0.7852 (p0) outliers start: 12 outliers final: 7 residues processed: 49 average time/residue: 0.7345 time to fit residues: 40.6690 Evaluate side-chains 46 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 267 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.133905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082594 restraints weight = 48780.327| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.01 r_work: 0.3133 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.7573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9852 Z= 0.110 Angle : 0.566 11.216 13381 Z= 0.278 Chirality : 0.044 0.211 1535 Planarity : 0.004 0.128 1735 Dihedral : 7.190 107.904 1718 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 0.97 % Allowed : 22.82 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 1.69 % 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: -1.11 (0.24), residues: 1206 helix: 1.49 (0.40), residues: 191 sheet: -1.16 (0.26), residues: 360 loop : -1.13 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 86 TYR 0.012 0.001 TYR A 661 PHE 0.013 0.001 PHE A 121 TRP 0.005 0.001 TRP B 230 HIS 0.002 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 9815) covalent geometry : angle 0.54292 / 0.27 (13287) SS BOND : bond 0.00355 / 0.20 ( 17) SS BOND : angle 1.48743 / 0.65 ( 34) hydrogen bonds : bond 0.02896 / 1.83 ( 306) hydrogen bonds : angle 5.35843 / 3.70 ( 810) link_ALPHA1-3 : bond 0.00940 / 0.45 ( 2) link_ALPHA1-3 : angle 2.40662 / 1.61 ( 6) link_ALPHA1-6 : bond 0.00799 / 0.38 ( 2) link_ALPHA1-6 : angle 1.47025 / 1.11 ( 6) link_BETA1-4 : bond 0.00263 / 0.13 ( 8) link_BETA1-4 : angle 2.00610 / 1.64 ( 24) link_NAG-ASN : bond 0.00625 / 0.38 ( 8) link_NAG-ASN : angle 2.46900 / 1.91 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7240.53 seconds wall clock time: 123 minutes 10.13 seconds (7390.13 seconds total)