Starting phenix.real_space_refine on Tue Mar 3 18:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d6a_27221/03_2026/8d6a_27221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d6a_27221/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8d6a_27221/03_2026/8d6a_27221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d6a_27221/03_2026/8d6a_27221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d6a_27221/03_2026/8d6a_27221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d6a_27221/03_2026/8d6a_27221.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.25, per 1000 atoms: 0.16 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: 0.62 Conformation dependent library (CDL) restraints added in 185.5 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: 0.37 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: 1.02 Time building geometry restraints manager: 0.77 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 - 21.50: 4729 21.50 - 43.00: 236 43.00 - 64.50: 55 64.50 - 86.00: 13 86.00 - 107.50: 34 Dihedral angle restraints: 5067 sinusoidal: 2227 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 5064 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: 3.900 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.000 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 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 : 16.683 107.504 3196 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 covalent geometry : bond 0.00276 ( 8111) covalent geometry : angle 0.55975 (11049) SS BOND : bond 0.00375 ( 9) SS BOND : angle 1.28266 ( 18) hydrogen bonds : bond 0.25047 ( 228) hydrogen bonds : angle 8.70376 ( 648) link_BETA1-4 : bond 0.00351 ( 5) link_BETA1-4 : angle 1.23252 ( 15) link_NAG-ASN : bond 0.00653 ( 10) link_NAG-ASN : angle 2.87550 ( 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 : 0.294 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: 0.0935 time to fit residues: 19.1549 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 : 0.308 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 404 ASN A 425 HIS B 158 ASN B 190 HIS B 479 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.121967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.099837 restraints weight = 22520.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099750 restraints weight = 14690.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.100510 restraints weight = 10896.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.100776 restraints weight = 10003.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.101007 restraints weight = 8697.391| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8135 Z= 0.154 Angle : 0.670 9.190 11112 Z= 0.328 Chirality : 0.047 0.300 1292 Planarity : 0.005 0.058 1374 Dihedral : 13.844 87.533 1346 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.18 % Allowed : 10.09 % Favored : 87.73 % 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: 2.07 (0.45), residues: 125 sheet: -1.49 (0.26), residues: 318 loop : -2.65 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 508 TYR 0.030 0.002 TYR A 396 PHE 0.016 0.001 PHE A 297 TRP 0.028 0.002 TRP B 172 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8111) covalent geometry : angle 0.65195 (11049) SS BOND : bond 0.00439 ( 9) SS BOND : angle 1.04488 ( 18) hydrogen bonds : bond 0.05271 ( 228) hydrogen bonds : angle 6.05118 ( 648) link_BETA1-4 : bond 0.00301 ( 5) link_BETA1-4 : angle 1.68939 ( 15) link_NAG-ASN : bond 0.00585 ( 10) link_NAG-ASN : angle 2.80857 ( 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 : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8511 (p0) cc_final: 0.8200 (p0) outliers start: 19 outliers final: 8 residues processed: 100 average time/residue: 0.0799 time to fit residues: 11.4763 Evaluate side-chains 89 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 503 THR 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: 0.8980 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.0020 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 0.0030 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 404 ASN A 478 HIS B 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.121141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.098898 restraints weight = 22235.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.098835 restraints weight = 14572.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.099347 restraints weight = 10829.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.099762 restraints weight = 10280.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.099972 restraints weight = 8826.944| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8135 Z= 0.120 Angle : 0.632 9.477 11112 Z= 0.306 Chirality : 0.045 0.355 1292 Planarity : 0.004 0.057 1374 Dihedral : 10.453 78.936 1346 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 1.95 % Allowed : 14.45 % Favored : 83.60 % 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: -2.04 (0.25), residues: 957 helix: 2.47 (0.46), residues: 125 sheet: -1.28 (0.26), residues: 330 loop : -2.49 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 154 TYR 0.012 0.001 TYR B 406 PHE 0.011 0.001 PHE A 297 TRP 0.032 0.001 TRP B 172 HIS 0.004 0.001 HIS D 41 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8111) covalent geometry : angle 0.61184 (11049) SS BOND : bond 0.00361 ( 9) SS BOND : angle 0.88295 ( 18) hydrogen bonds : bond 0.05049 ( 228) hydrogen bonds : angle 5.49597 ( 648) link_BETA1-4 : bond 0.00412 ( 5) link_BETA1-4 : angle 1.52131 ( 15) link_NAG-ASN : bond 0.00672 ( 10) link_NAG-ASN : angle 2.92921 ( 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 107 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8506 (p0) cc_final: 0.8137 (p0) REVERT: B 469 GLU cc_start: 0.4626 (OUTLIER) cc_final: 0.4368 (pt0) outliers start: 17 outliers final: 10 residues processed: 100 average time/residue: 0.0757 time to fit residues: 10.7023 Evaluate side-chains 93 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 258 ASN Chi-restraints excluded: chain A residue 350 VAL 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 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: 2.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** 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 = 0.4016 r_free = 0.4016 target = 0.118055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.096210 restraints weight = 22505.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.095913 restraints weight = 15237.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.096310 restraints weight = 13451.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.096803 restraints weight = 10982.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.096917 restraints weight = 9867.095| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8135 Z= 0.142 Angle : 0.628 9.609 11112 Z= 0.309 Chirality : 0.046 0.354 1292 Planarity : 0.004 0.056 1374 Dihedral : 8.917 71.773 1346 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.75 % Allowed : 14.91 % Favored : 82.34 % 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: -1.84 (0.26), residues: 957 helix: 2.55 (0.46), residues: 122 sheet: -1.05 (0.26), residues: 328 loop : -2.39 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 176 TYR 0.013 0.001 TYR B 406 PHE 0.012 0.001 PHE A 297 TRP 0.020 0.002 TRP B 172 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8111) covalent geometry : angle 0.60585 (11049) SS BOND : bond 0.00486 ( 9) SS BOND : angle 1.21830 ( 18) hydrogen bonds : bond 0.05589 ( 228) hydrogen bonds : angle 5.38589 ( 648) link_BETA1-4 : bond 0.00324 ( 5) link_BETA1-4 : angle 1.60304 ( 15) link_NAG-ASN : bond 0.00637 ( 10) link_NAG-ASN : angle 2.98335 ( 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 111 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 LEU cc_start: 0.9148 (tp) cc_final: 0.8939 (tp) REVERT: A 177 ASP cc_start: 0.8435 (p0) cc_final: 0.8090 (p0) REVERT: B 442 LYS cc_start: 0.7327 (mmmt) cc_final: 0.7126 (mmmt) REVERT: B 453 TRP cc_start: 0.6239 (p90) cc_final: 0.5951 (p90) REVERT: B 469 GLU cc_start: 0.4754 (OUTLIER) cc_final: 0.4504 (pt0) outliers start: 24 outliers final: 14 residues processed: 103 average time/residue: 0.0851 time to fit residues: 12.1938 Evaluate side-chains 93 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR 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 402 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 482 LEU 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 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: 7.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4005 r_free = 0.4005 target = 0.117289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.095611 restraints weight = 22345.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.095276 restraints weight = 15160.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.095702 restraints weight = 13328.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.096189 restraints weight = 10830.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.096291 restraints weight = 9760.501| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3404 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= 0.133 Angle : 0.643 9.913 11112 Z= 0.312 Chirality : 0.045 0.339 1292 Planarity : 0.004 0.056 1374 Dihedral : 8.431 68.150 1346 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.21 % Allowed : 15.94 % Favored : 80.85 % 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: -1.71 (0.26), residues: 957 helix: 2.10 (0.47), residues: 131 sheet: -0.89 (0.27), residues: 328 loop : -2.27 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 176 TYR 0.017 0.001 TYR A 366 PHE 0.011 0.001 PHE A 297 TRP 0.037 0.001 TRP B 172 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8111) covalent geometry : angle 0.62084 (11049) SS BOND : bond 0.00522 ( 9) SS BOND : angle 1.24858 ( 18) hydrogen bonds : bond 0.05625 ( 228) hydrogen bonds : angle 5.19490 ( 648) link_BETA1-4 : bond 0.00392 ( 5) link_BETA1-4 : angle 1.63649 ( 15) link_NAG-ASN : bond 0.00649 ( 10) link_NAG-ASN : angle 3.00756 ( 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 109 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 LEU cc_start: 0.9163 (tp) cc_final: 0.8962 (tp) REVERT: A 177 ASP cc_start: 0.8506 (p0) cc_final: 0.8104 (p0) REVERT: B 453 TRP cc_start: 0.6219 (p90) cc_final: 0.5977 (p90) REVERT: B 464 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6401 (t80) outliers start: 28 outliers final: 19 residues processed: 98 average time/residue: 0.0821 time to fit residues: 11.4487 Evaluate side-chains 94 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR 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 368 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain B residue 209 MET 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 464 PHE 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: 1.9990 chunk 45 optimal weight: 6.9990 chunk 50 optimal weight: 0.0000 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 GLN A 258 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3998 r_free = 0.3998 target = 0.116710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.094857 restraints weight = 22184.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.094874 restraints weight = 15122.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.095265 restraints weight = 12745.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.095728 restraints weight = 10737.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.095822 restraints weight = 9731.155| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8135 Z= 0.128 Angle : 0.628 9.453 11112 Z= 0.303 Chirality : 0.045 0.332 1292 Planarity : 0.004 0.055 1374 Dihedral : 7.885 63.468 1346 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.33 % Allowed : 16.17 % Favored : 80.50 % 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: -1.69 (0.27), residues: 957 helix: 2.09 (0.47), residues: 131 sheet: -0.93 (0.27), residues: 335 loop : -2.23 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 395 TYR 0.013 0.001 TYR A 396 PHE 0.010 0.001 PHE A 297 TRP 0.027 0.002 TRP B 172 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8111) covalent geometry : angle 0.60553 (11049) SS BOND : bond 0.00430 ( 9) SS BOND : angle 1.20227 ( 18) hydrogen bonds : bond 0.05505 ( 228) hydrogen bonds : angle 5.01464 ( 648) link_BETA1-4 : bond 0.00398 ( 5) link_BETA1-4 : angle 1.69592 ( 15) link_NAG-ASN : bond 0.00634 ( 10) link_NAG-ASN : angle 2.98791 ( 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 109 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 62 LEU cc_start: 0.9165 (tp) cc_final: 0.8948 (tp) REVERT: A 176 ARG cc_start: 0.7928 (mpt-90) cc_final: 0.7603 (tpp-160) REVERT: A 177 ASP cc_start: 0.8487 (p0) cc_final: 0.8141 (p0) REVERT: B 453 TRP cc_start: 0.6219 (p90) cc_final: 0.5982 (p90) REVERT: B 464 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6415 (t80) outliers start: 29 outliers final: 20 residues processed: 98 average time/residue: 0.0794 time to fit residues: 11.0110 Evaluate side-chains 94 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR 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 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 145 SER 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 464 PHE 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: 0.6980 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.109410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086328 restraints weight = 22407.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.086510 restraints weight = 19083.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086849 restraints weight = 13516.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087342 restraints weight = 11876.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087381 restraints weight = 10649.772| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8135 Z= 0.249 Angle : 0.790 20.307 11112 Z= 0.387 Chirality : 0.049 0.334 1292 Planarity : 0.006 0.061 1374 Dihedral : 8.165 61.183 1346 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 3.44 % Allowed : 16.97 % 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: -1.91 (0.26), residues: 957 helix: 1.91 (0.45), residues: 127 sheet: -1.02 (0.27), residues: 339 loop : -2.39 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 395 TYR 0.019 0.002 TYR A 257 PHE 0.014 0.002 PHE A 297 TRP 0.024 0.003 TRP B 172 HIS 0.004 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 8111) covalent geometry : angle 0.76857 (11049) SS BOND : bond 0.00738 ( 9) SS BOND : angle 1.69788 ( 18) hydrogen bonds : bond 0.08468 ( 228) hydrogen bonds : angle 5.60214 ( 648) link_BETA1-4 : bond 0.00504 ( 5) link_BETA1-4 : angle 2.00031 ( 15) link_NAG-ASN : bond 0.00611 ( 10) link_NAG-ASN : angle 3.16414 ( 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: 30 poor density : 74 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7573 (mt) REVERT: A 177 ASP cc_start: 0.8508 (p0) cc_final: 0.8279 (p0) REVERT: B 469 GLU cc_start: 0.4814 (OUTLIER) cc_final: 0.4324 (pt0) outliers start: 30 outliers final: 21 residues processed: 93 average time/residue: 0.0813 time to fit residues: 10.7613 Evaluate side-chains 91 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 204 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 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 145 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS ** 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 = 0.3903 r_free = 0.3903 target = 0.111363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088532 restraints weight = 22509.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.088878 restraints weight = 17409.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089176 restraints weight = 13135.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089671 restraints weight = 11377.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089731 restraints weight = 10179.956| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8135 Z= 0.153 Angle : 0.874 32.669 11112 Z= 0.378 Chirality : 0.061 1.416 1292 Planarity : 0.005 0.057 1374 Dihedral : 8.086 58.206 1346 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.75 % Allowed : 18.58 % Favored : 78.67 % 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: 1.84 (0.47), residues: 131 sheet: -0.96 (0.28), residues: 331 loop : -2.30 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 395 TYR 0.017 0.001 TYR A 257 PHE 0.011 0.001 PHE A 297 TRP 0.024 0.002 TRP B 172 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8111) covalent geometry : angle 0.73900 (11049) SS BOND : bond 0.00586 ( 9) SS BOND : angle 1.52691 ( 18) hydrogen bonds : bond 0.06929 ( 228) hydrogen bonds : angle 5.28950 ( 648) link_BETA1-4 : bond 0.00444 ( 5) link_BETA1-4 : angle 1.82934 ( 15) link_NAG-ASN : bond 0.00616 ( 10) link_NAG-ASN : angle 8.87465 ( 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 93 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7433 (mt) REVERT: A 177 ASP cc_start: 0.8489 (p0) cc_final: 0.8182 (p0) REVERT: B 469 GLU cc_start: 0.4758 (OUTLIER) cc_final: 0.3973 (pt0) outliers start: 24 outliers final: 20 residues processed: 85 average time/residue: 0.0822 time to fit residues: 9.9570 Evaluate side-chains 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR 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 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 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 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: 5.9990 chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 0.0000 chunk 13 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.117027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.095465 restraints weight = 22723.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.096446 restraints weight = 16703.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.096813 restraints weight = 12693.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.097243 restraints weight = 9278.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.097307 restraints weight = 8202.824| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8135 Z= 0.136 Angle : 0.807 29.949 11112 Z= 0.358 Chirality : 0.047 0.367 1292 Planarity : 0.005 0.056 1374 Dihedral : 7.416 55.394 1346 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 3.33 % Allowed : 17.78 % Favored : 78.90 % 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: -1.74 (0.27), residues: 957 helix: 1.99 (0.47), residues: 131 sheet: -0.95 (0.28), residues: 333 loop : -2.24 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 176 TYR 0.010 0.001 TYR B 505 PHE 0.011 0.001 PHE A 297 TRP 0.031 0.002 TRP A 470 HIS 0.002 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8111) covalent geometry : angle 0.69693 (11049) SS BOND : bond 0.00542 ( 9) SS BOND : angle 1.41666 ( 18) hydrogen bonds : bond 0.06318 ( 228) hydrogen bonds : angle 5.15590 ( 648) link_BETA1-4 : bond 0.00490 ( 5) link_BETA1-4 : angle 1.83024 ( 15) link_NAG-ASN : bond 0.00746 ( 10) link_NAG-ASN : angle 7.70903 ( 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 101 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7305 (mt) REVERT: A 177 ASP cc_start: 0.8409 (p0) cc_final: 0.8062 (p0) REVERT: B 469 GLU cc_start: 0.4602 (OUTLIER) cc_final: 0.3789 (pt0) outliers start: 29 outliers final: 22 residues processed: 93 average time/residue: 0.0756 time to fit residues: 9.9354 Evaluate side-chains 87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 87 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 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 415 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 41 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4066 r_free = 0.4066 target = 0.118309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.095595 restraints weight = 22727.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095638 restraints weight = 17010.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.095998 restraints weight = 11942.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096449 restraints weight = 10621.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.096695 restraints weight = 9147.042| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8135 Z= 0.149 Angle : 0.771 22.810 11112 Z= 0.353 Chirality : 0.047 0.336 1292 Planarity : 0.005 0.056 1374 Dihedral : 7.368 55.947 1346 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.52 % Allowed : 19.15 % Favored : 78.33 % 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: -1.71 (0.27), residues: 957 helix: 2.00 (0.47), residues: 131 sheet: -0.95 (0.28), residues: 334 loop : -2.22 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 395 TYR 0.010 0.001 TYR A 492 PHE 0.010 0.001 PHE A 297 TRP 0.052 0.002 TRP A 470 HIS 0.002 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8111) covalent geometry : angle 0.69981 (11049) SS BOND : bond 0.00579 ( 9) SS BOND : angle 1.45305 ( 18) hydrogen bonds : bond 0.06386 ( 228) hydrogen bonds : angle 5.19231 ( 648) link_BETA1-4 : bond 0.00497 ( 5) link_BETA1-4 : angle 1.91859 ( 15) link_NAG-ASN : bond 0.00733 ( 10) link_NAG-ASN : angle 6.07749 ( 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 94 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7361 (mt) REVERT: A 177 ASP cc_start: 0.8485 (p0) cc_final: 0.8142 (p0) REVERT: B 469 GLU cc_start: 0.4602 (OUTLIER) cc_final: 0.3867 (pt0) outliers start: 22 outliers final: 20 residues processed: 87 average time/residue: 0.0779 time to fit residues: 9.5853 Evaluate side-chains 89 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 CYS Chi-restraints excluded: chain D residue 67 TYR 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 287 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 402 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.0000 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3918 r_free = 0.3918 target = 0.112142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.086590 restraints weight = 22199.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.088965 restraints weight = 11433.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090451 restraints weight = 7725.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.091322 restraints weight = 6070.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.091758 restraints weight = 5268.498| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4954 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= 0.132 Angle : 0.752 22.499 11112 Z= 0.345 Chirality : 0.046 0.336 1292 Planarity : 0.005 0.055 1374 Dihedral : 7.363 59.740 1346 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 2.64 % Allowed : 19.15 % 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: -1.60 (0.27), residues: 957 helix: 2.07 (0.47), residues: 131 sheet: -0.85 (0.29), residues: 322 loop : -2.14 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 176 TYR 0.032 0.001 TYR A 492 PHE 0.010 0.001 PHE A 297 TRP 0.045 0.002 TRP A 470 HIS 0.003 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8111) covalent geometry : angle 0.68394 (11049) SS BOND : bond 0.00530 ( 9) SS BOND : angle 1.35257 ( 18) hydrogen bonds : bond 0.05893 ( 228) hydrogen bonds : angle 5.07770 ( 648) link_BETA1-4 : bond 0.00498 ( 5) link_BETA1-4 : angle 1.89461 ( 15) link_NAG-ASN : bond 0.00785 ( 10) link_NAG-ASN : angle 5.83661 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1577.02 seconds wall clock time: 27 minutes 52.17 seconds (1672.17 seconds total)