Starting phenix.real_space_refine on Thu Jul 2 09:09:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d6a_27221/07_2026/8d6a_27221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d6a_27221/07_2026/8d6a_27221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d6a_27221/07_2026/8d6a_27221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d6a_27221/07_2026/8d6a_27221.map" model { file = "/net/cci-nas-00/data/ceres_data/8d6a_27221/07_2026/8d6a_27221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d6a_27221/07_2026/8d6a_27221.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d6a_27221/07_2026/8d6a_27221.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d6a_27221/07_2026/8d6a_27221.cif" } resolution = 3.54 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5043 2.51 5 N 1321 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7912 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3167 Classifications: {'peptide': 392} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain: "B" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3225 Classifications: {'peptide': 402} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 381} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.64, per 1000 atoms: 0.21 Number of scatterers: 7912 At special positions: 0 Unit cell: (104.06, 141.04, 160.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1516 8.00 N 1321 7.00 C 5043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 351 " distance=2.04 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 511 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 701 " - " ASN A 131 " " NAG A 702 " - " ASN A 390 " " NAG A 703 " - " ASN A 157 " " NAG A 704 " - " ASN A 383 " " NAG A 705 " - " ASN A 379 " " NAG C 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 407 " " NAG F 1 " - " ASN B 426 " " NAG G 1 " - " ASN B 303 " " NAG H 1 " - " ASN B 243 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 446.3 milliseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 21 sheets defined 13.8% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'D' and resid 43 through 70 Processing helix chain 'D' and resid 72 through 77 removed outlier: 4.404A pdb=" N ASN D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 77 " --> pdb=" O PRO D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 77' Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 97 through 127 Processing helix chain 'D' and resid 131 through 159 Processing helix chain 'D' and resid 176 through 202 removed outlier: 3.792A pdb=" N GLN D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.956A pdb=" N SER A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 144 removed outlier: 9.418A pdb=" N LYS A 221 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 196 removed outlier: 3.733A pdb=" N PHE A 214 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 196 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 212 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 removed outlier: 3.561A pdb=" N VAL A 207 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 226 through 232 removed outlier: 6.149A pdb=" N ASN A 227 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR A 245 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 231 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 271 Processing sheet with id=AA7, first strand: chain 'A' and resid 332 through 336 removed outlier: 3.790A pdb=" N ARG A 345 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 389 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 349 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 380 removed outlier: 3.573A pdb=" N LEU A 370 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR A 396 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 416 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.956A pdb=" N PHE A 433 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 440 " --> pdb=" O PHE A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 473 removed outlier: 3.556A pdb=" N GLN A 471 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 455 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 497 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 473 removed outlier: 3.556A pdb=" N GLN A 471 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 455 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 497 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 492 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 512 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 508 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AB4, first strand: chain 'B' and resid 143 through 147 removed outlier: 3.738A pdb=" N ASN B 143 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 192 removed outlier: 3.837A pdb=" N ASN B 169 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 173 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 221 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 175 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 219 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 244 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 218 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 242 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.658A pdb=" N ILE B 267 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 301 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 297 " --> pdb=" O CYS B 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 259 through 262 removed outlier: 6.299A pdb=" N LYS B 259 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY B 330 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE B 261 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 323 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 312 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 279 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 337 through 340 removed outlier: 3.657A pdb=" N GLN B 337 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 354 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU B 339 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N SER B 352 " --> pdb=" O LEU B 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 348 through 350 Processing sheet with id=AC1, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.627A pdb=" N TYR B 406 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 419 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 437 through 440 removed outlier: 3.761A pdb=" N HIS B 454 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE B 439 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER B 452 " --> pdb=" O PHE B 439 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 477 through 481 removed outlier: 3.823A pdb=" N ARG B 480 " --> pdb=" O ILE B 468 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 648 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: 1.28 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2485 1.35 - 1.47: 2021 1.47 - 1.59: 3565 1.59 - 1.71: 0 1.71 - 1.83: 40 Bond restraints: 8111 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 8106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 10742 1.55 - 3.10: 270 3.10 - 4.64: 30 4.64 - 6.19: 5 6.19 - 7.74: 2 Bond angle restraints: 11049 Sorted by residual: angle pdb=" C GLU A 151 " pdb=" N THR A 152 " pdb=" CA THR A 152 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C LYS A 130 " pdb=" N ASN A 131 " pdb=" CA ASN A 131 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.96e+00 angle pdb=" C ASN A 131 " pdb=" N LEU A 132 " pdb=" CA LEU A 132 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.21e+00 angle pdb=" CA TYR D 67 " pdb=" CB TYR D 67 " pdb=" CG TYR D 67 " ideal model delta sigma weight residual 113.90 118.23 -4.33 1.80e+00 3.09e-01 5.78e+00 angle pdb=" N THR A 166 " pdb=" CA THR A 166 " pdb=" C THR A 166 " ideal model delta sigma weight residual 113.18 110.18 3.00 1.33e+00 5.65e-01 5.10e+00 ... (remaining 11044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4388 17.80 - 35.60: 308 35.60 - 53.41: 42 53.41 - 71.21: 9 71.21 - 89.01: 5 Dihedral angle restraints: 4752 sinusoidal: 1912 harmonic: 2840 Sorted by residual: dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual 93.00 141.21 -48.21 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CA ASN A 131 " pdb=" C ASN A 131 " pdb=" N LEU A 132 " pdb=" CA LEU A 132 " ideal model delta harmonic sigma weight residual 180.00 155.57 24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA THR B 447 " pdb=" C THR B 447 " pdb=" N ALA B 448 " pdb=" CA ALA B 448 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 4749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1116 0.065 - 0.130: 168 0.130 - 0.195: 6 0.195 - 0.260: 0 0.260 - 0.324: 2 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 390 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 383 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 131 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1289 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 500 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO B 501 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 325 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 326 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 445 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 446 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 446 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 446 " -0.019 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1725 2.79 - 3.32: 7108 3.32 - 3.84: 12077 3.84 - 4.37: 13247 4.37 - 4.90: 23412 Nonbonded interactions: 57569 Sorted by model distance: nonbonded pdb=" O ILE A 454 " pdb=" OG1 THR A 497 " model vdw 2.261 3.040 nonbonded pdb=" O HIS A 425 " pdb=" OH TYR A 500 " model vdw 2.263 3.040 nonbonded pdb=" O SER A 133 " pdb=" N GLU A 145 " model vdw 2.277 3.120 nonbonded pdb=" O ILE D 64 " pdb=" OG1 THR D 68 " model vdw 2.292 3.040 nonbonded pdb=" O SER B 473 " pdb=" OG SER B 473 " model vdw 2.302 3.040 ... (remaining 57564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8135 Z= 0.143 Angle : 0.582 8.908 11112 Z= 0.292 Chirality : 0.044 0.324 1292 Planarity : 0.004 0.063 1374 Dihedral : 12.093 89.010 2881 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.24), residues: 957 helix: 1.02 (0.44), residues: 124 sheet: -1.81 (0.27), residues: 308 loop : -2.98 (0.22), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 372 TYR 0.017 0.001 TYR D 67 PHE 0.005 0.000 PHE A 332 TRP 0.004 0.000 TRP B 517 HIS 0.004 0.000 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 8111) covalent geometry : angle 0.55975 / 0.29 (11049) SS BOND : bond 0.00375 / 0.27 ( 9) SS BOND : angle 1.28266 / 0.84 ( 18) hydrogen bonds : bond 0.25047 / 17.40 ( 228) hydrogen bonds : angle 8.70376 / 5.91 ( 648) link_BETA1-4 : bond 0.00351 / 0.19 ( 5) link_BETA1-4 : angle 1.23252 / 0.95 ( 15) link_NAG-ASN : bond 0.00653 / 0.36 ( 10) link_NAG-ASN : angle 2.87550 / 2.32 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8500 (p0) cc_final: 0.8173 (p0) REVERT: B 442 LYS cc_start: 0.7751 (tppt) cc_final: 0.7530 (tppt) REVERT: B 503 THR cc_start: 0.6822 (m) cc_final: 0.6186 (m) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0813 time to fit residues: 16.6886 Evaluate side-chains 90 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN D 70 GLN D 76 ASN D 193 GLN A 153 HIS A 167 HIS A 258 ASN A 342 GLN A 360 ASN A 376 HIS A 404 ASN A 425 HIS B 158 ASN B 190 HIS B 479 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.122002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.100126 restraints weight = 22506.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.100210 restraints weight = 16010.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.100694 restraints weight = 11894.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.101105 restraints weight = 10644.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.101386 restraints weight = 9153.609| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8135 Z= 0.149 Angle : 0.625 9.025 11112 Z= 0.314 Chirality : 0.045 0.320 1292 Planarity : 0.005 0.059 1374 Dihedral : 4.020 24.680 1031 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.18 % Allowed : 9.86 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.25), residues: 957 helix: 2.06 (0.46), residues: 125 sheet: -1.50 (0.26), residues: 318 loop : -2.64 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 121 TYR 0.027 0.002 TYR A 396 PHE 0.013 0.001 PHE A 297 TRP 0.027 0.002 TRP B 172 HIS 0.002 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8111) covalent geometry : angle 0.60639 / 0.31 (11049) SS BOND : bond 0.00433 / 0.31 ( 9) SS BOND : angle 1.06337 / 0.75 ( 18) hydrogen bonds : bond 0.05576 / 4.02 ( 228) hydrogen bonds : angle 6.09027 / 4.13 ( 648) link_BETA1-4 : bond 0.00308 / 0.15 ( 5) link_BETA1-4 : angle 1.29159 / 0.97 ( 15) link_NAG-ASN : bond 0.00496 / 0.31 ( 10) link_NAG-ASN : angle 2.82481 / 2.26 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8467 (p0) cc_final: 0.8151 (p0) outliers start: 19 outliers final: 7 residues processed: 100 average time/residue: 0.0715 time to fit residues: 10.1541 Evaluate side-chains 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS B 190 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.112649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090138 restraints weight = 22369.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.090352 restraints weight = 17785.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090664 restraints weight = 13017.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.091152 restraints weight = 11286.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.091197 restraints weight = 10136.052| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8135 Z= 0.234 Angle : 0.747 11.917 11112 Z= 0.379 Chirality : 0.048 0.309 1292 Planarity : 0.006 0.062 1374 Dihedral : 5.031 31.402 1031 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.52 % Allowed : 15.48 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.25), residues: 957 helix: 1.55 (0.46), residues: 132 sheet: -1.37 (0.25), residues: 341 loop : -2.56 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 221 TYR 0.028 0.003 TYR A 396 PHE 0.017 0.002 PHE A 332 TRP 0.036 0.003 TRP B 172 HIS 0.008 0.001 HIS D 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 ( 8111) covalent geometry : angle 0.72705 / 0.38 (11049) SS BOND : bond 0.01257 / 0.68 ( 9) SS BOND : angle 1.42138 / 0.99 ( 18) hydrogen bonds : bond 0.08575 / 6.35 ( 228) hydrogen bonds : angle 5.91971 / 4.09 ( 648) link_BETA1-4 : bond 0.00356 / 0.18 ( 5) link_BETA1-4 : angle 1.53073 / 1.11 ( 15) link_NAG-ASN : bond 0.00558 / 0.32 ( 10) link_NAG-ASN : angle 3.09617 / 2.44 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7514 (mt) REVERT: A 177 ASP cc_start: 0.8433 (p0) cc_final: 0.8054 (p0) REVERT: B 453 TRP cc_start: 0.6392 (p90) cc_final: 0.6080 (p90) REVERT: B 469 GLU cc_start: 0.4980 (OUTLIER) cc_final: 0.4653 (pt0) outliers start: 22 outliers final: 9 residues processed: 101 average time/residue: 0.0780 time to fit residues: 11.0136 Evaluate side-chains 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.114192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.092347 restraints weight = 22571.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.092009 restraints weight = 19094.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.092551 restraints weight = 13851.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093024 restraints weight = 11626.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.093143 restraints weight = 10578.339| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8135 Z= 0.139 Angle : 0.637 9.368 11112 Z= 0.319 Chirality : 0.045 0.320 1292 Planarity : 0.005 0.057 1374 Dihedral : 4.651 29.809 1031 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.21 % Allowed : 16.86 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.26), residues: 957 helix: 1.88 (0.47), residues: 131 sheet: -1.12 (0.27), residues: 335 loop : -2.33 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 178 TYR 0.014 0.001 TYR A 366 PHE 0.011 0.001 PHE A 297 TRP 0.017 0.001 TRP B 172 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8111) covalent geometry : angle 0.61397 / 0.31 (11049) SS BOND : bond 0.00628 / 0.43 ( 9) SS BOND : angle 1.39407 / 0.89 ( 18) hydrogen bonds : bond 0.06721 / 4.98 ( 228) hydrogen bonds : angle 5.51872 / 3.81 ( 648) link_BETA1-4 : bond 0.00370 / 0.19 ( 5) link_BETA1-4 : angle 1.31622 / 0.98 ( 15) link_NAG-ASN : bond 0.00588 / 0.33 ( 10) link_NAG-ASN : angle 3.07980 / 2.45 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7334 (mt) REVERT: A 177 ASP cc_start: 0.8404 (p0) cc_final: 0.8006 (p0) REVERT: B 442 LYS cc_start: 0.7551 (tppt) cc_final: 0.7332 (tppt) REVERT: B 469 GLU cc_start: 0.4918 (OUTLIER) cc_final: 0.4580 (pt0) outliers start: 28 outliers final: 18 residues processed: 96 average time/residue: 0.0733 time to fit residues: 10.1324 Evaluate side-chains 86 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 51 GLN A 258 ASN A 404 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.111536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089308 restraints weight = 22600.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089133 restraints weight = 18385.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.089760 restraints weight = 13398.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.090180 restraints weight = 11343.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.090236 restraints weight = 10329.683| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8135 Z= 0.186 Angle : 0.691 10.398 11112 Z= 0.342 Chirality : 0.046 0.318 1292 Planarity : 0.005 0.056 1374 Dihedral : 4.870 31.568 1031 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 3.67 % Allowed : 16.74 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.27), residues: 957 helix: 1.70 (0.46), residues: 131 sheet: -1.02 (0.28), residues: 329 loop : -2.35 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 176 TYR 0.012 0.002 TYR A 453 PHE 0.011 0.001 PHE A 297 TRP 0.020 0.002 TRP A 470 HIS 0.003 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 8111) covalent geometry : angle 0.66750 / 0.34 (11049) SS BOND : bond 0.00507 / 0.30 ( 9) SS BOND : angle 1.55634 / 1.01 ( 18) hydrogen bonds : bond 0.07415 / 5.52 ( 228) hydrogen bonds : angle 5.53221 / 3.84 ( 648) link_BETA1-4 : bond 0.00354 / 0.18 ( 5) link_BETA1-4 : angle 1.48287 / 1.08 ( 15) link_NAG-ASN : bond 0.00548 / 0.31 ( 10) link_NAG-ASN : angle 3.16011 / 2.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 MET cc_start: 0.7442 (mmm) cc_final: 0.7189 (mmm) REVERT: A 132 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7530 (mt) REVERT: A 177 ASP cc_start: 0.8478 (p0) cc_final: 0.8193 (p0) REVERT: A 395 ARG cc_start: 0.6206 (mtt180) cc_final: 0.5988 (ttm110) REVERT: B 469 GLU cc_start: 0.5055 (OUTLIER) cc_final: 0.4725 (pt0) outliers start: 32 outliers final: 22 residues processed: 98 average time/residue: 0.0748 time to fit residues: 10.3949 Evaluate side-chains 92 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 0.0070 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.112819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090672 restraints weight = 22221.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090990 restraints weight = 16018.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.091288 restraints weight = 12472.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.091775 restraints weight = 10773.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.091808 restraints weight = 9700.290| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8135 Z= 0.134 Angle : 0.658 16.088 11112 Z= 0.320 Chirality : 0.045 0.324 1292 Planarity : 0.004 0.057 1374 Dihedral : 4.724 30.340 1031 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 3.33 % Allowed : 17.32 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.27), residues: 957 helix: 1.92 (0.47), residues: 131 sheet: -0.88 (0.28), residues: 328 loop : -2.25 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 178 TYR 0.008 0.001 TYR A 334 PHE 0.010 0.001 PHE B 459 TRP 0.016 0.001 TRP B 172 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8111) covalent geometry : angle 0.63518 / 0.31 (11049) SS BOND : bond 0.00540 / 0.37 ( 9) SS BOND : angle 1.44237 / 0.93 ( 18) hydrogen bonds : bond 0.06521 / 4.85 ( 228) hydrogen bonds : angle 5.31412 / 3.68 ( 648) link_BETA1-4 : bond 0.00372 / 0.19 ( 5) link_BETA1-4 : angle 1.31168 / 0.96 ( 15) link_NAG-ASN : bond 0.00577 / 0.33 ( 10) link_NAG-ASN : angle 3.14553 / 2.49 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7421 (mt) REVERT: A 177 ASP cc_start: 0.8495 (p0) cc_final: 0.8204 (p0) REVERT: B 469 GLU cc_start: 0.5061 (OUTLIER) cc_final: 0.4794 (pt0) outliers start: 29 outliers final: 22 residues processed: 91 average time/residue: 0.0732 time to fit residues: 9.3857 Evaluate side-chains 90 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.110103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.088156 restraints weight = 23248.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.087903 restraints weight = 16339.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.088540 restraints weight = 12569.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.088889 restraints weight = 11176.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089051 restraints weight = 10333.540| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 8135 Z= 0.355 Angle : 0.882 12.239 11112 Z= 0.444 Chirality : 0.052 0.324 1292 Planarity : 0.006 0.062 1374 Dihedral : 5.821 35.843 1031 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 4.24 % Allowed : 17.55 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.26), residues: 957 helix: 1.30 (0.45), residues: 125 sheet: -1.17 (0.28), residues: 338 loop : -2.51 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 176 TYR 0.020 0.003 TYR A 492 PHE 0.015 0.002 PHE B 217 TRP 0.019 0.003 TRP A 373 HIS 0.006 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00840 / 0.36 ( 8111) covalent geometry : angle 0.85801 / 0.44 (11049) SS BOND : bond 0.00933 / 0.59 ( 9) SS BOND : angle 2.20455 / 1.39 ( 18) hydrogen bonds : bond 0.10284 / 7.74 ( 228) hydrogen bonds : angle 6.28565 / 4.42 ( 648) link_BETA1-4 : bond 0.00609 / 0.30 ( 5) link_BETA1-4 : angle 1.83678 / 1.33 ( 15) link_NAG-ASN : bond 0.00595 / 0.34 ( 10) link_NAG-ASN : angle 3.48260 / 2.67 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8499 (p0) cc_final: 0.8172 (p0) REVERT: B 167 ARG cc_start: 0.7099 (mpp-170) cc_final: 0.6814 (ttm110) REVERT: B 469 GLU cc_start: 0.5530 (OUTLIER) cc_final: 0.5042 (pt0) outliers start: 37 outliers final: 25 residues processed: 98 average time/residue: 0.0749 time to fit residues: 10.4210 Evaluate side-chains 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.114307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.092187 restraints weight = 23276.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.092804 restraints weight = 15825.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.093318 restraints weight = 11435.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.093663 restraints weight = 10061.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.093806 restraints weight = 9282.455| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8135 Z= 0.153 Angle : 0.716 11.802 11112 Z= 0.354 Chirality : 0.047 0.335 1292 Planarity : 0.005 0.059 1374 Dihedral : 5.245 31.881 1031 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.87 % Allowed : 19.38 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.27), residues: 957 helix: 1.88 (0.47), residues: 125 sheet: -1.02 (0.28), residues: 337 loop : -2.30 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 178 TYR 0.013 0.001 TYR A 334 PHE 0.011 0.001 PHE B 459 TRP 0.018 0.002 TRP A 351 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8111) covalent geometry : angle 0.69220 / 0.35 (11049) SS BOND : bond 0.00720 / 0.50 ( 9) SS BOND : angle 1.69517 / 1.08 ( 18) hydrogen bonds : bond 0.07444 / 5.54 ( 228) hydrogen bonds : angle 5.65169 / 3.96 ( 648) link_BETA1-4 : bond 0.00400 / 0.20 ( 5) link_BETA1-4 : angle 1.41761 / 1.03 ( 15) link_NAG-ASN : bond 0.00588 / 0.34 ( 10) link_NAG-ASN : angle 3.27068 / 2.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8468 (p0) cc_final: 0.8114 (p0) REVERT: A 352 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8540 (mmtt) REVERT: B 469 GLU cc_start: 0.5254 (OUTLIER) cc_final: 0.4952 (pt0) outliers start: 25 outliers final: 20 residues processed: 93 average time/residue: 0.0748 time to fit residues: 9.9571 Evaluate side-chains 89 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.109314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086625 restraints weight = 22018.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.087127 restraints weight = 16138.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.087374 restraints weight = 11685.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087734 restraints weight = 10767.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087806 restraints weight = 9106.443| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8135 Z= 0.164 Angle : 0.718 10.975 11112 Z= 0.351 Chirality : 0.046 0.334 1292 Planarity : 0.005 0.060 1374 Dihedral : 5.120 31.777 1031 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 2.98 % Allowed : 19.61 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.27), residues: 957 helix: 2.01 (0.46), residues: 125 sheet: -1.06 (0.28), residues: 332 loop : -2.22 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 178 TYR 0.011 0.001 TYR A 453 PHE 0.011 0.001 PHE B 459 TRP 0.017 0.002 TRP A 351 HIS 0.003 0.001 HIS B 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8111) covalent geometry : angle 0.69440 / 0.35 (11049) SS BOND : bond 0.00669 / 0.45 ( 9) SS BOND : angle 1.67872 / 1.09 ( 18) hydrogen bonds : bond 0.07179 / 5.34 ( 228) hydrogen bonds : angle 5.50001 / 3.85 ( 648) link_BETA1-4 : bond 0.00342 / 0.18 ( 5) link_BETA1-4 : angle 1.51493 / 1.10 ( 15) link_NAG-ASN : bond 0.00555 / 0.32 ( 10) link_NAG-ASN : angle 3.21142 / 2.51 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8505 (p0) cc_final: 0.8158 (p0) REVERT: B 394 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7119 (mp-120) REVERT: B 469 GLU cc_start: 0.5250 (OUTLIER) cc_final: 0.4946 (pt0) outliers start: 26 outliers final: 21 residues processed: 95 average time/residue: 0.0712 time to fit residues: 9.6805 Evaluate side-chains 92 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 0.0370 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.110852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087954 restraints weight = 21800.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088817 restraints weight = 15949.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089543 restraints weight = 10984.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089782 restraints weight = 9121.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089930 restraints weight = 8627.745| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8135 Z= 0.131 Angle : 0.710 10.343 11112 Z= 0.345 Chirality : 0.046 0.334 1292 Planarity : 0.005 0.059 1374 Dihedral : 4.981 30.681 1031 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 2.75 % Allowed : 20.07 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.27), residues: 957 helix: 2.21 (0.47), residues: 125 sheet: -1.02 (0.28), residues: 339 loop : -2.11 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 178 TYR 0.011 0.001 TYR B 393 PHE 0.012 0.001 PHE B 459 TRP 0.020 0.001 TRP A 470 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8111) covalent geometry : angle 0.68815 / 0.34 (11049) SS BOND : bond 0.00570 / 0.39 ( 9) SS BOND : angle 1.50530 / 0.98 ( 18) hydrogen bonds : bond 0.06368 / 4.73 ( 228) hydrogen bonds : angle 5.31082 / 3.71 ( 648) link_BETA1-4 : bond 0.00376 / 0.20 ( 5) link_BETA1-4 : angle 1.39786 / 1.01 ( 15) link_NAG-ASN : bond 0.00592 / 0.34 ( 10) link_NAG-ASN : angle 3.17170 / 2.50 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8000 (mmm-85) cc_final: 0.7780 (mmt180) REVERT: A 177 ASP cc_start: 0.8516 (p0) cc_final: 0.8162 (p0) REVERT: B 469 GLU cc_start: 0.5206 (OUTLIER) cc_final: 0.4939 (pt0) outliers start: 24 outliers final: 20 residues processed: 88 average time/residue: 0.0661 time to fit residues: 8.4367 Evaluate side-chains 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 TRP Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 469 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 513 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 75 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 25 optimal weight: 0.0570 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.111840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.086517 restraints weight = 22130.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088886 restraints weight = 11418.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090345 restraints weight = 7721.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.091218 restraints weight = 6064.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.091767 restraints weight = 5229.505| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8135 Z= 0.121 Angle : 0.684 10.164 11112 Z= 0.332 Chirality : 0.045 0.336 1292 Planarity : 0.005 0.059 1374 Dihedral : 4.722 28.927 1031 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.52 % Allowed : 20.30 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.28), residues: 957 helix: 2.08 (0.47), residues: 131 sheet: -0.89 (0.28), residues: 334 loop : -2.07 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 178 TYR 0.010 0.001 TYR B 505 PHE 0.010 0.001 PHE B 459 TRP 0.017 0.001 TRP B 172 HIS 0.003 0.000 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8111) covalent geometry : angle 0.66257 / 0.33 (11049) SS BOND : bond 0.00481 / 0.32 ( 9) SS BOND : angle 1.36609 / 0.90 ( 18) hydrogen bonds : bond 0.05351 / 3.96 ( 228) hydrogen bonds : angle 4.99337 / 3.49 ( 648) link_BETA1-4 : bond 0.00316 / 0.17 ( 5) link_BETA1-4 : angle 1.28335 / 0.94 ( 15) link_NAG-ASN : bond 0.00603 / 0.35 ( 10) link_NAG-ASN : angle 3.09929 / 2.46 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.40 seconds wall clock time: 26 minutes 29.60 seconds (1589.60 seconds total)