Starting phenix.real_space_refine on Fri Oct 23 03:04:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zub_74802/10_2026/9zub_74802.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zub_74802/10_2026/9zub_74802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zub_74802/10_2026/9zub_74802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zub_74802/10_2026/9zub_74802.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zub_74802/10_2026/9zub_74802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zub_74802/10_2026/9zub_74802.map" } resolution = 3.65 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 66 5.16 5 C 4914 2.51 5 N 1358 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2887 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 369, 2879 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 16, 'TRANS': 352} Conformer: "B" Number of residues, atoms: 369, 2879 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 16, 'TRANS': 352} bond proxies already assigned to first conformer: 2935 Chain: "B" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1874 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain: "C" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3035 Classifications: {'peptide': 381} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 368} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Planarities with less than four sites: {'CGU:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' CA': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 2.09, per 1000 atoms: 0.27 Number of scatterers: 7860 At special positions: 0 Unit cell: (107.648, 95.584, 127.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 66 16.00 O 1514 8.00 N 1358 7.00 C 4914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 2 " - pdb=" SG CYS A 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 58 " distance=2.02 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 414 " distance=2.04 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 23 " distance=2.03 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 71 " distance=2.04 Simple disulfide: pdb=" SG CYS C 73 " - pdb=" SG CYS C 82 " distance=2.03 Simple disulfide: pdb=" SG CYS C 88 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 206 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 361 " - pdb=" SG CYS C 389 " 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 NAG-ASN " NAG A 401 " - " ASN A 72 " " NAG A 402 " - " ASN A 108 " " NAG B 701 " - " ASN B 432 " " NAG B 702 " - " ASN B 473 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 546.3 milliseconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 14 sheets defined 15.5% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.594A pdb=" N ALA A 176 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 215 removed outlier: 3.654A pdb=" N CYS A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.682A pdb=" N CYS B 414 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 432 through 436 removed outlier: 3.585A pdb=" N ILE B 436 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 531 Processing helix chain 'B' and resid 596 through 605 Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 24 through 33 removed outlier: 3.514A pdb=" N ALA C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL C 31 " --> pdb=" O CGU C 27 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 46 Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 292 through 302 removed outlier: 4.059A pdb=" N PHE C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'C' and resid 404 through 412 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.566A pdb=" N THR A 44 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 57 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR A 18 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.947A pdb=" N ILE A 146 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN A 108 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N HIS A 151 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN A 106 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 4.188A pdb=" N ARG A 159 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.559A pdb=" N LEU A 236 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS A 237 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 199 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A 239 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 195 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 191 through 192 Processing sheet with id=AA7, first strand: chain 'A' and resid 277 through 283 removed outlier: 5.562A pdb=" N GLY A 347 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ASP A 282 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ARG A 345 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS A 328 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 290 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 330 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 424 through 428 removed outlier: 3.993A pdb=" N CYS B 398 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR B 389 " --> pdb=" O HIS B 396 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS B 396 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 465 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE B 448 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS B 467 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 515 through 518 removed outlier: 4.024A pdb=" N THR B 499 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU B 561 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 572 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 576 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL B 589 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS B 542 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 65 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB3, first strand: chain 'C' and resid 115 through 117 Processing sheet with id=AB4, first strand: chain 'C' and resid 185 through 186 removed outlier: 3.610A pdb=" N GLU C 185 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N SER C 304 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU C 372 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 308 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS C 369 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE C 383 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR C 399 " --> pdb=" O ILE C 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 195 through 200 removed outlier: 4.252A pdb=" N CYS C 206 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG C 252 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 250 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE C 229 " --> pdb=" O VAL C 250 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2581 1.34 - 1.46: 1927 1.46 - 1.59: 3445 1.59 - 1.71: 0 1.71 - 1.83: 74 Bond restraints: 8027 Sorted by residual: bond pdb=" N CYS C 82 " pdb=" CA CYS C 82 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.39e-02 5.18e+03 3.53e+00 bond pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CB GLN C 139 " pdb=" CG GLN C 139 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CB MET B 540 " pdb=" CG MET B 540 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CB GLU C 239 " pdb=" CG GLU C 239 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.45e+00 ... (remaining 8022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 10459 1.81 - 3.63: 345 3.63 - 5.44: 54 5.44 - 7.25: 9 7.25 - 9.07: 4 Bond angle restraints: 10871 Sorted by residual: angle pdb=" C VAL A 31 " pdb=" N CYS A 32 " pdb=" CA CYS A 32 " ideal model delta sigma weight residual 122.26 115.83 6.43 1.73e+00 3.34e-01 1.38e+01 angle pdb=" C ASN A 72 " pdb=" N ARG A 73 " pdb=" CA ARG A 73 " ideal model delta sigma weight residual 123.00 118.26 4.74 1.38e+00 5.25e-01 1.18e+01 angle pdb=" C ALA C 187 " pdb=" N LYS C 188 " pdb=" CA LYS C 188 " ideal model delta sigma weight residual 120.49 124.85 -4.36 1.42e+00 4.96e-01 9.43e+00 angle pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " pdb=" C5 NAG B 701 " ideal model delta sigma weight residual 113.21 122.28 -9.07 3.00e+00 1.11e-01 9.14e+00 angle pdb=" N TRP C 385 " pdb=" CA TRP C 385 " pdb=" C TRP C 385 " ideal model delta sigma weight residual 107.73 111.66 -3.93 1.34e+00 5.57e-01 8.60e+00 ... (remaining 10866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 4441 18.11 - 36.22: 355 36.22 - 54.34: 67 54.34 - 72.45: 19 72.45 - 90.56: 8 Dihedral angle restraints: 4890 sinusoidal: 2049 harmonic: 2841 Sorted by residual: dihedral pdb=" CB CYS A 208 " pdb=" SG CYS A 208 " pdb=" SG CYS A 237 " pdb=" CB CYS A 237 " ideal model delta sinusoidal sigma weight residual -86.00 -157.74 71.74 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 175 " pdb=" CB CYS A 175 " ideal model delta sinusoidal sigma weight residual 93.00 26.42 66.58 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CB CYS B 398 " pdb=" SG CYS B 398 " pdb=" SG CYS B 414 " pdb=" CB CYS B 414 " ideal model delta sinusoidal sigma weight residual 93.00 37.49 55.51 1 1.00e+01 1.00e-02 4.16e+01 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1087 0.092 - 0.184: 98 0.184 - 0.276: 5 0.276 - 0.367: 0 0.367 - 0.459: 1 Chirality restraints: 1191 Sorted by residual: chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 108 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" C2 NAG B 701 " pdb=" C1 NAG B 701 " pdb=" C3 NAG B 701 " pdb=" N2 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.23 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 473 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1188 not shown) Planarity restraints: 1405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 315 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 316 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 316 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 316 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 432 " 0.003 2.00e-02 2.50e+03 2.23e-02 6.22e+00 pdb=" CG ASN B 432 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 432 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 432 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 72 " 0.001 2.00e-02 2.50e+03 2.08e-02 5.42e+00 pdb=" CG ASN A 72 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 72 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN A 72 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.023 2.00e-02 2.50e+03 ... (remaining 1402 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 559 2.74 - 3.28: 8116 3.28 - 3.82: 12820 3.82 - 4.36: 15731 4.36 - 4.90: 26371 Nonbonded interactions: 63597 Sorted by model distance: nonbonded pdb="OE21 CGU C 20 " pdb="CA CA C 507 " model vdw 2.196 2.510 nonbonded pdb="OE21 CGU C 36 " pdb="CA CA C 508 " model vdw 2.245 2.510 nonbonded pdb="OE11 CGU C 17 " pdb="CA CA C 503 " model vdw 2.253 2.510 nonbonded pdb="OE22 CGU C 8 " pdb="CA CA C 501 " model vdw 2.255 2.510 nonbonded pdb=" OD1 ASP A 185 " pdb="CA CA C 506 " model vdw 2.262 2.510 ... (remaining 63592 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.004 0.044 8058 Z= 0.187 Angle : 0.844 17.187 10937 Z= 0.436 Chirality : 0.053 0.459 1191 Planarity : 0.005 0.074 1401 Dihedral : 13.472 90.559 2987 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.23 % Allowed : 0.12 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.27), residues: 950 helix: -1.01 (0.47), residues: 114 sheet: -0.27 (0.33), residues: 241 loop : -0.46 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 504 TYR 0.027 0.002 TYR A 34 PHE 0.023 0.002 PHE C 130 TRP 0.015 0.002 TRP C 310 HIS 0.009 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 8027) covalent geometry : angle 0.78712 / 0.42 (10871) SS BOND : bond 0.00335 / 0.21 ( 27) SS BOND : angle 1.50711 / 0.80 ( 54) hydrogen bonds : bond 0.13522 / 8.18 ( 223) hydrogen bonds : angle 7.72653 / 5.21 ( 576) link_NAG-ASN : bond 0.01422 / 0.74 ( 4) link_NAG-ASN : angle 8.78700 / 5.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.308 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 10 THR cc_start: 0.8864 (m) cc_final: 0.8536 (p) REVERT: A 62 ASP cc_start: 0.8286 (t70) cc_final: 0.8080 (t0) REVERT: A 116 GLN cc_start: 0.7662 (tt0) cc_final: 0.7197 (tm-30) REVERT: A 280 ASP cc_start: 0.8581 (t0) cc_final: 0.8169 (t0) REVERT: A 290 ILE cc_start: 0.9259 (mp) cc_final: 0.8987 (mt) REVERT: A 314 TYR cc_start: 0.8903 (t80) cc_final: 0.8455 (t80) REVERT: B 462 ASP cc_start: 0.8953 (t0) cc_final: 0.8550 (t0) REVERT: C 265 LYS cc_start: 0.7508 (pttp) cc_final: 0.7271 (tppt) REVERT: C 292 ASP cc_start: 0.6550 (m-30) cc_final: 0.5357 (p0) REVERT: C 348 MET cc_start: 0.8020 (ttm) cc_final: 0.7256 (ttm) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0865 time to fit residues: 16.7122 Evaluate side-chains 76 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS B 528 GLN C 191 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.137536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.087432 restraints weight = 30143.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087381 restraints weight = 14722.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089398 restraints weight = 8251.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.089928 restraints weight = 5738.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.090061 restraints weight = 4921.057| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8058 Z= 0.159 Angle : 0.725 14.965 10937 Z= 0.362 Chirality : 0.050 0.386 1191 Planarity : 0.004 0.051 1401 Dihedral : 7.292 62.208 1187 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.47 % Allowed : 7.51 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.27), residues: 950 helix: -0.44 (0.47), residues: 115 sheet: -0.27 (0.32), residues: 251 loop : -0.45 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 504 TYR 0.021 0.002 TYR C 284 PHE 0.025 0.002 PHE A 43 TRP 0.014 0.002 TRP C 72 HIS 0.005 0.001 HIS B 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8027) covalent geometry : angle 0.67898 / 0.35 (10871) SS BOND : bond 0.00289 / 0.18 ( 27) SS BOND : angle 1.25293 / 0.68 ( 54) hydrogen bonds : bond 0.03561 / 2.26 ( 223) hydrogen bonds : angle 6.08757 / 4.13 ( 576) link_NAG-ASN : bond 0.01352 / 0.70 ( 4) link_NAG-ASN : angle 7.41004 / 4.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.324 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 62 ASP cc_start: 0.8110 (t70) cc_final: 0.7868 (t0) REVERT: A 116 GLN cc_start: 0.7558 (tt0) cc_final: 0.7245 (tm-30) REVERT: A 280 ASP cc_start: 0.8186 (t0) cc_final: 0.7669 (t0) REVERT: A 314 TYR cc_start: 0.8930 (t80) cc_final: 0.8520 (t80) REVERT: C 130 PHE cc_start: 0.7212 (m-80) cc_final: 0.6985 (m-80) REVERT: C 191 GLN cc_start: 0.7664 (tm130) cc_final: 0.6999 (tm-30) REVERT: C 292 ASP cc_start: 0.6366 (m-30) cc_final: 0.5664 (t0) REVERT: C 295 TYR cc_start: 0.5916 (m-10) cc_final: 0.5669 (m-10) REVERT: C 348 MET cc_start: 0.7616 (ttm) cc_final: 0.7271 (ttm) outliers start: 2 outliers final: 1 residues processed: 93 average time/residue: 0.0893 time to fit residues: 11.5746 Evaluate side-chains 77 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [63, 33, 90, 17, 10, 14, 25, 79, 64, 31, 28] chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 64 optimal weight: 0.0040 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.134806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081188 restraints weight = 21396.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.083601 restraints weight = 10318.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085166 restraints weight = 6524.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085860 restraints weight = 4981.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.086404 restraints weight = 4370.123| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8058 Z= 0.197 Angle : 0.694 14.541 10937 Z= 0.349 Chirality : 0.049 0.413 1191 Planarity : 0.004 0.044 1401 Dihedral : 6.872 51.230 1187 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.41 % Allowed : 9.39 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.27), residues: 950 helix: -0.11 (0.48), residues: 114 sheet: -0.41 (0.32), residues: 254 loop : -0.42 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 327 TYR 0.014 0.002 TYR C 306 PHE 0.029 0.002 PHE A 131 TRP 0.012 0.001 TRP B 577 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 8027) covalent geometry : angle 0.64685 / 0.34 (10871) SS BOND : bond 0.00374 / 0.24 ( 27) SS BOND : angle 1.23582 / 0.68 ( 54) hydrogen bonds : bond 0.03507 / 2.28 ( 223) hydrogen bonds : angle 5.93427 / 4.03 ( 576) link_NAG-ASN : bond 0.01259 / 0.65 ( 4) link_NAG-ASN : angle 7.27563 / 4.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.304 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 10 THR cc_start: 0.9001 (p) cc_final: 0.8709 (t) REVERT: A 116 GLN cc_start: 0.7559 (tt0) cc_final: 0.7262 (tm-30) REVERT: A 280 ASP cc_start: 0.8190 (t0) cc_final: 0.7594 (t0) REVERT: A 314 TYR cc_start: 0.9091 (t80) cc_final: 0.8851 (t80) REVERT: A 325 LYS cc_start: 0.8585 (mptt) cc_final: 0.8369 (mmtt) REVERT: C 191 GLN cc_start: 0.7530 (tm130) cc_final: 0.7117 (tm-30) REVERT: C 195 GLN cc_start: 0.6598 (tp-100) cc_final: 0.6337 (tp-100) REVERT: C 265 LYS cc_start: 0.7962 (pttp) cc_final: 0.7621 (tppt) REVERT: C 292 ASP cc_start: 0.6249 (m-30) cc_final: 0.5924 (t0) REVERT: C 348 MET cc_start: 0.7578 (ttm) cc_final: 0.7077 (ttm) outliers start: 10 outliers final: 9 residues processed: 84 average time/residue: 0.0964 time to fit residues: 11.1551 Evaluate side-chains 79 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [59, 33, 44, 17, 62, 21, 36, 19, 2, 76, 35] chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.133065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079317 restraints weight = 22084.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081778 restraints weight = 10041.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083342 restraints weight = 6270.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.084210 restraints weight = 4772.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.084923 restraints weight = 4134.580| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8058 Z= 0.212 Angle : 0.699 14.178 10937 Z= 0.352 Chirality : 0.049 0.414 1191 Planarity : 0.004 0.040 1401 Dihedral : 6.710 52.770 1187 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.88 % Allowed : 10.33 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.27), residues: 950 helix: -0.02 (0.48), residues: 114 sheet: -0.49 (0.32), residues: 252 loop : -0.39 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 73 TYR 0.016 0.002 TYR A 34 PHE 0.030 0.002 PHE A 131 TRP 0.009 0.001 TRP B 577 HIS 0.006 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 ( 8027) covalent geometry : angle 0.65175 / 0.34 (10871) SS BOND : bond 0.00357 / 0.22 ( 27) SS BOND : angle 1.31284 / 0.75 ( 54) hydrogen bonds : bond 0.03354 / 2.20 ( 223) hydrogen bonds : angle 5.86999 / 3.99 ( 576) link_NAG-ASN : bond 0.01198 / 0.61 ( 4) link_NAG-ASN : angle 7.23914 / 4.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.7683 (tt0) cc_final: 0.7426 (tm-30) REVERT: A 280 ASP cc_start: 0.8483 (t0) cc_final: 0.7791 (t0) REVERT: A 314 TYR cc_start: 0.9138 (t80) cc_final: 0.8910 (t80) REVERT: A 325 LYS cc_start: 0.8366 (mptt) cc_final: 0.8091 (mptt) REVERT: B 512 ASN cc_start: 0.8774 (p0) cc_final: 0.8167 (p0) REVERT: C 195 GLN cc_start: 0.6638 (tp-100) cc_final: 0.6396 (tp-100) REVERT: C 265 LYS cc_start: 0.7907 (pttp) cc_final: 0.7547 (tppt) REVERT: C 292 ASP cc_start: 0.6183 (m-30) cc_final: 0.5860 (t0) REVERT: C 348 MET cc_start: 0.7739 (ttm) cc_final: 0.7195 (ttm) REVERT: C 364 ASP cc_start: 0.6242 (t0) cc_final: 0.5981 (t0) outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 0.0841 time to fit residues: 9.5343 Evaluate side-chains 68 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [15, 26, 2, 85, 69, 32, 86, 89, 92, 55, 95] chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 HIS A 235 ASN ** B 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN C 139 GLN C 354 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.128925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.075015 restraints weight = 21349.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077228 restraints weight = 9926.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078598 restraints weight = 6375.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079570 restraints weight = 5007.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.080040 restraints weight = 4292.978| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 8058 Z= 0.345 Angle : 0.798 14.150 10937 Z= 0.410 Chirality : 0.052 0.396 1191 Planarity : 0.005 0.045 1401 Dihedral : 6.678 48.165 1187 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.11 % Allowed : 11.03 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.27), residues: 950 helix: -0.23 (0.47), residues: 115 sheet: -0.55 (0.33), residues: 248 loop : -0.50 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 70 TYR 0.023 0.002 TYR A 27 PHE 0.030 0.003 PHE A 131 TRP 0.024 0.002 TRP C 72 HIS 0.008 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.35 ( 8027) covalent geometry : angle 0.75382 / 0.40 (10871) SS BOND : bond 0.00526 / 0.32 ( 27) SS BOND : angle 1.69226 / 0.96 ( 54) hydrogen bonds : bond 0.03890 / 2.56 ( 223) hydrogen bonds : angle 6.22411 / 4.19 ( 576) link_NAG-ASN : bond 0.01040 / 0.53 ( 4) link_NAG-ASN : angle 7.29048 / 4.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8831 (m-80) cc_final: 0.8502 (m-80) REVERT: A 272 PHE cc_start: 0.8411 (m-80) cc_final: 0.8131 (m-80) REVERT: A 280 ASP cc_start: 0.8545 (t0) cc_final: 0.8016 (t0) REVERT: C 191 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7680 (pp30) REVERT: C 348 MET cc_start: 0.7779 (ttm) cc_final: 0.7193 (ttm) outliers start: 16 outliers final: 13 residues processed: 64 average time/residue: 0.0785 time to fit residues: 7.2790 Evaluate side-chains 55 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [36, 18, 83, 85, 25, 10, 70, 40, 94, 6, 91] chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 40 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS C 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.133239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084738 restraints weight = 33395.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.082265 restraints weight = 14995.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.083589 restraints weight = 9951.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.084519 restraints weight = 7333.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.085138 restraints weight = 6696.319| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8058 Z= 0.125 Angle : 0.641 12.885 10937 Z= 0.327 Chirality : 0.047 0.429 1191 Planarity : 0.004 0.034 1401 Dihedral : 6.233 48.406 1187 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.41 % Allowed : 13.15 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.27), residues: 950 helix: -0.12 (0.48), residues: 120 sheet: -0.41 (0.33), residues: 247 loop : -0.47 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.020 0.001 TYR A 314 PHE 0.026 0.002 PHE A 43 TRP 0.008 0.001 TRP B 501 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8027) covalent geometry : angle 0.60013 / 0.32 (10871) SS BOND : bond 0.00248 / 0.17 ( 27) SS BOND : angle 1.03383 / 0.60 ( 54) hydrogen bonds : bond 0.03028 / 2.01 ( 223) hydrogen bonds : angle 5.77017 / 3.95 ( 576) link_NAG-ASN : bond 0.01248 / 0.63 ( 4) link_NAG-ASN : angle 6.59966 / 3.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.8455 (t0) cc_final: 0.7805 (t0) REVERT: A 314 TYR cc_start: 0.8668 (t80) cc_final: 0.8462 (t80) REVERT: C 81 ASN cc_start: 0.8203 (t0) cc_final: 0.7893 (t0) REVERT: C 292 ASP cc_start: 0.6300 (m-30) cc_final: 0.6028 (t0) REVERT: C 348 MET cc_start: 0.7726 (ttm) cc_final: 0.7122 (ttm) outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 0.0740 time to fit residues: 7.0913 Evaluate side-chains 59 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [17, 47, 24, 53, 91, 87, 61, 93, 69, 45, 1] chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 HIS C 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.130020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075993 restraints weight = 21675.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.078280 restraints weight = 10117.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.079808 restraints weight = 6383.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080633 restraints weight = 4910.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081340 restraints weight = 4274.989| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8058 Z= 0.253 Angle : 0.704 12.902 10937 Z= 0.361 Chirality : 0.049 0.413 1191 Planarity : 0.004 0.036 1401 Dihedral : 6.230 42.634 1187 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.90 % Favored : 93.99 % Rotamer: Outliers : 1.41 % Allowed : 14.55 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.27), residues: 950 helix: -0.14 (0.47), residues: 121 sheet: -0.45 (0.34), residues: 245 loop : -0.50 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 73 TYR 0.020 0.002 TYR A 314 PHE 0.021 0.002 PHE A 43 TRP 0.015 0.001 TRP B 577 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 ( 8027) covalent geometry : angle 0.66167 / 0.35 (10871) SS BOND : bond 0.00458 / 0.30 ( 27) SS BOND : angle 1.47281 / 0.85 ( 54) hydrogen bonds : bond 0.03425 / 2.28 ( 223) hydrogen bonds : angle 5.92568 / 3.99 ( 576) link_NAG-ASN : bond 0.00984 / 0.50 ( 4) link_NAG-ASN : angle 6.69531 / 3.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.8462 (t0) cc_final: 0.8020 (t0) REVERT: C 81 ASN cc_start: 0.8560 (t0) cc_final: 0.8088 (t0) REVERT: C 348 MET cc_start: 0.7743 (ttm) cc_final: 0.7045 (ttm) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.0803 time to fit residues: 6.4784 Evaluate side-chains 49 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [66, 38, 63, 80, 94, 11, 53, 6, 21, 0, 34] chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.132327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078556 restraints weight = 21862.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080891 restraints weight = 9972.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082436 restraints weight = 6310.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083357 restraints weight = 4842.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.083879 restraints weight = 4165.317| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8058 Z= 0.150 Angle : 0.637 12.058 10937 Z= 0.326 Chirality : 0.047 0.419 1191 Planarity : 0.004 0.035 1401 Dihedral : 6.006 45.535 1187 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.37 % Favored : 94.52 % Rotamer: Outliers : 1.29 % Allowed : 14.91 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.27), residues: 950 helix: -0.10 (0.47), residues: 121 sheet: -0.48 (0.34), residues: 236 loop : -0.41 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 94 TYR 0.014 0.001 TYR A 314 PHE 0.024 0.002 PHE A 43 TRP 0.009 0.001 TRP B 577 HIS 0.004 0.001 HIS C 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8027) covalent geometry : angle 0.59800 / 0.32 (10871) SS BOND : bond 0.00300 / 0.20 ( 27) SS BOND : angle 1.14551 / 0.66 ( 54) hydrogen bonds : bond 0.03022 / 2.01 ( 223) hydrogen bonds : angle 5.70956 / 3.89 ( 576) link_NAG-ASN : bond 0.01097 / 0.55 ( 4) link_NAG-ASN : angle 6.27766 / 3.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8985 (m-80) cc_final: 0.8693 (m-80) REVERT: A 280 ASP cc_start: 0.8418 (t0) cc_final: 0.7719 (t0) REVERT: C 81 ASN cc_start: 0.8496 (t0) cc_final: 0.8051 (t0) REVERT: C 348 MET cc_start: 0.7707 (ttm) cc_final: 0.6977 (ttm) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.0864 time to fit residues: 6.7900 Evaluate side-chains 56 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [59, 5, 89, 17, 95, 69, 19, 16, 84, 56, 13] chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS C 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.131556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080398 restraints weight = 29736.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.080434 restraints weight = 16982.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.082625 restraints weight = 8971.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083711 restraints weight = 6176.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.083862 restraints weight = 5494.815| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8058 Z= 0.167 Angle : 0.646 12.242 10937 Z= 0.331 Chirality : 0.047 0.411 1191 Planarity : 0.004 0.035 1401 Dihedral : 5.943 44.396 1187 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 0.94 % Allowed : 15.02 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.28), residues: 950 helix: -0.07 (0.48), residues: 121 sheet: -0.47 (0.35), residues: 236 loop : -0.38 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.015 0.001 TYR A 314 PHE 0.023 0.002 PHE A 43 TRP 0.011 0.001 TRP B 577 HIS 0.004 0.001 HIS C 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 8027) covalent geometry : angle 0.60971 / 0.32 (10871) SS BOND : bond 0.00341 / 0.23 ( 27) SS BOND : angle 1.19495 / 0.69 ( 54) hydrogen bonds : bond 0.03013 / 2.00 ( 223) hydrogen bonds : angle 5.67868 / 3.86 ( 576) link_NAG-ASN : bond 0.01022 / 0.51 ( 4) link_NAG-ASN : angle 6.14196 / 3.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.8243 (t0) cc_final: 0.7619 (t0) REVERT: C 81 ASN cc_start: 0.8430 (t0) cc_final: 0.8014 (t0) REVERT: C 348 MET cc_start: 0.7740 (ttm) cc_final: 0.6833 (tpt) outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 0.0794 time to fit residues: 6.1951 Evaluate side-chains 54 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [37, 81, 10, 80, 95, 24, 67, 54, 20, 16, 12] chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.132545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.079295 restraints weight = 22830.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081601 restraints weight = 10606.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.083051 restraints weight = 6751.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.084094 restraints weight = 5231.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.084562 restraints weight = 4468.791| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8058 Z= 0.137 Angle : 0.625 12.022 10937 Z= 0.320 Chirality : 0.047 0.405 1191 Planarity : 0.004 0.035 1401 Dihedral : 5.789 45.761 1187 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.37 % Favored : 94.52 % Rotamer: Outliers : 1.17 % Allowed : 14.67 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.28), residues: 950 helix: -0.03 (0.48), residues: 121 sheet: -0.41 (0.35), residues: 236 loop : -0.34 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.014 0.001 TYR A 314 PHE 0.023 0.002 PHE A 43 TRP 0.012 0.001 TRP C 72 HIS 0.004 0.001 HIS C 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8027) covalent geometry : angle 0.59040 / 0.31 (10871) SS BOND : bond 0.00281 / 0.19 ( 27) SS BOND : angle 1.09491 / 0.63 ( 54) hydrogen bonds : bond 0.02862 / 1.89 ( 223) hydrogen bonds : angle 5.58267 / 3.81 ( 576) link_NAG-ASN : bond 0.01063 / 0.53 ( 4) link_NAG-ASN : angle 5.90122 / 3.42 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.8132 (t0) cc_final: 0.7573 (t0) REVERT: A 314 TYR cc_start: 0.8806 (t80) cc_final: 0.8480 (t80) REVERT: C 81 ASN cc_start: 0.8383 (t0) cc_final: 0.7795 (t0) REVERT: C 292 ASP cc_start: 0.6158 (m-30) cc_final: 0.5910 (t0) REVERT: C 348 MET cc_start: 0.7692 (ttm) cc_final: 0.6790 (tpt) REVERT: C 364 ASP cc_start: 0.6688 (t0) cc_final: 0.6208 (t0) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.0769 time to fit residues: 7.0132 Evaluate side-chains 60 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain B residue 556 ASP Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: [66, 96, 39, 13, 34, 42, 43, 44, 29, 0, 57] chunk 66 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.131787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078939 restraints weight = 22248.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081269 restraints weight = 10438.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082769 restraints weight = 6687.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.083445 restraints weight = 5123.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.083971 restraints weight = 4509.077| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8058 Z= 0.160 Angle : 0.635 12.231 10937 Z= 0.326 Chirality : 0.047 0.395 1191 Planarity : 0.004 0.035 1401 Dihedral : 5.759 43.659 1187 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.69 % Favored : 94.20 % Rotamer: Outliers : 1.17 % Allowed : 15.02 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.28), residues: 950 helix: -0.02 (0.48), residues: 121 sheet: -0.42 (0.35), residues: 236 loop : -0.29 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 73 TYR 0.016 0.001 TYR A 314 PHE 0.023 0.002 PHE A 43 TRP 0.011 0.001 TRP B 577 HIS 0.004 0.001 HIS C 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8027) covalent geometry : angle 0.60152 / 0.32 (10871) SS BOND : bond 0.00317 / 0.21 ( 27) SS BOND : angle 1.18044 / 0.68 ( 54) hydrogen bonds : bond 0.02904 / 1.93 ( 223) hydrogen bonds : angle 5.58663 / 3.80 ( 576) link_NAG-ASN : bond 0.00975 / 0.49 ( 4) link_NAG-ASN : angle 5.79787 / 3.34 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1859.06 seconds wall clock time: 32 minutes 33.82 seconds (1953.82 seconds total)